score:2

Accepted answer

What you're asking is too complicated for a D3 nest. Besides that, d3.nest is about to be deprecated anyway... So, here is a pure JavaScript approach.

We first get a collection of unique years:

const yearsList = [...new Set(data.map(d => d.years.map(e => e.year)).flat())];

Then, with that collection in hand, we loop through your data and create a new array (here called newData), in a solution which is purposely both ad hoc and verbose:

yearsList.forEach(d => {
  data.forEach(e => {

    const foundObject = e.years.find(f => f.year === d);

    if (foundObject) {

      const foundInNewData = newData.find(f => f.year === d);

      const values = {
        name: e.name,
        code: e.code,
        description: e.description,
        target: foundObject.target,
        weeks: foundObject.weeks
      };

      if (foundInNewData) {
        foundInNewData.values.push(values);
      } else {
        newData.push({
          year: d,
          values: [values]
        });
      };

    };

  });
});

And here is the demo:

const data = [{
    "id": 2,
    "name": "Test activity 51",
    "code": "D51",
    "description": "Description goes here.",
    "years": [{
        "id": 8,
        "year": "2020-2021",
        "target": 65,
        "weeks": [{
            "week_ending": "2020-12-06",
            "hours": 4.0
          },
          {
            "week_ending": "2020-12-06",
            "hours": 2.5
          },
          {
            "week_ending": "2020-10-18",
            "hours": 2.0
          },
          {
            "week_ending": "2020-07-19",
            "hours": 2.0
          }
        ]
      },
      {
        "id": 11,
        "year": "2019-2020",
        "target": 40,
        "weeks": [{
            "week_ending": "2020-01-05",
            "hours": 3.0
          },
          {
            "week_ending": "2019-09-15",
            "hours": 5.5
          },
          {
            "week_ending": "2019-07-14",
            "hours": 1.5
          }
        ]
      },
      {
        "id": 10,
        "year": "2018-2019",
        "target": 40,
        "weeks": [{
          "week_ending": "2018-09-30",
          "hours": 3.0
        }]
      }
    ]
  },
  {
    "id": 3,
    "name": "Test activity 63",
    "code": "D63",
    "description": null,
    "years": [{
        "id": 2,
        "year": "2019-2020",
        "target": 15,
        "weeks": [{
            "week_ending": "2020-05-24",
            "hours": 2.0
          },
          {
            "week_ending": "2020-03-22",
            "hours": 4.0
          },
          {
            "week_ending": "2020-01-26",
            "hours": 5.0
          },
          {
            "week_ending": "2020-01-19",
            "hours": 4.0
          },
          {
            "week_ending": "2019-12-01",
            "hours": 4.5
          },
          {
            "week_ending": "2019-08-25",
            "hours": 2.0
          },
          {
            "week_ending": "2019-07-21",
            "hours": 3.0
          }
        ]
      },
      {
        "id": 9,
        "year": "2018-2019",
        "target": 30,
        "weeks": [{
            "week_ending": "2018-08-19",
            "hours": 3.5
          },
          {
            "week_ending": "2019-02-10",
            "hours": 5.0
          },
          {
            "week_ending": "2018-12-30",
            "hours": 3.0
          },
          {
            "week_ending": "2018-10-21",
            "hours": 2.0
          },
          {
            "week_ending": "2018-08-26",
            "hours": 4.0
          }
        ]
      }
    ]
  },
  {
    "id": 1,
    "name": "Test activity 27",
    "code": "D27",
    "description": "Description goes here.",
    "years": [{
        "id": 4,
        "year": "2019-2020",
        "target": 30,
        "weeks": [{
            "week_ending": "2020-04-05",
            "hours": 2.0
          },
          {
            "week_ending": "2020-03-22",
            "hours": 6.0
          },
          {
            "week_ending": "2020-01-12",
            "hours": 1.0
          }
        ]
      },
      {
        "id": 1,
        "year": "2018-2019",
        "target": 25,
        "weeks": [{
            "week_ending": "2018-11-18",
            "hours": 6.0
          },
          {
            "week_ending": "2018-10-21",
            "hours": 2.0
          },
          {
            "week_ending": "2018-10-07",
            "hours": 6.0
          }
        ]
      }
    ]
  },
  {
    "id": 10,
    "name": "Test activity 59",
    "code": "D59",
    "description": null,
    "years": [{
        "id": 13,
        "year": "2020-2021",
        "target": 15,
        "weeks": [{
            "week_ending": "2021-04-18",
            "hours": 4.0
          },
          {
            "week_ending": "2021-02-28",
            "hours": 2.0
          },
          {
            "week_ending": "2021-02-14",
            "hours": 5.0
          },
          {
            "week_ending": "2020-11-22",
            "hours": 3.0
          },
          {
            "week_ending": "2020-08-16",
            "hours": 2.0
          }
        ]
      },
      {
        "id": 14,
        "year": "2019-2020",
        "target": 18,
        "weeks": [{
            "week_ending": "2019-12-01",
            "hours": 2.0
          },
          {
            "week_ending": "2019-10-27",
            "hours": 9.0
          },
          {
            "week_ending": "2019-09-01",
            "hours": 2.5
          }
        ]
      },
      {
        "id": 12,
        "year": "2018-2019",
        "target": 20,
        "weeks": [{
            "week_ending": "2018-11-11",
            "hours": 4.0
          },
          {
            "week_ending": "2018-08-26",
            "hours": 1.0
          },
          {
            "week_ending": "2018-08-12",
            "hours": 12.0
          }
        ]
      }
    ]
  }
];

const yearsList = [...new Set(data.map(d => d.years.map(e => e.year)).flat())];

const newData = [];

yearsList.forEach(d => {
  data.forEach(e => {
    const foundObject = e.years.find(f => f.year === d);
    if (foundObject) {
      const foundInNewData = newData.find(f => f.year === d);
      const values = {
        name: e.name,
        code: e.code,
        description: e.description,
        target: foundObject.target,
        weeks: foundObject.weeks
      };
      if (foundInNewData) {
        foundInNewData.values.push(values)
      } else {
        newData.push({
          year: d,
          values: [values]
        })
      }
    }
  })
});

console.log(newData)
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/5.7.0/d3.min.js"></script>

As you'll notice, the code above has not just one or two, but three loops. If your data array is too big you can also try a solution with just two nested loops:

const newData = [];

data.forEach(d => {
  d.years.forEach(e => {
    const foundInNewData = newData.find(f => f.year === e.year);
    const values = {
      name: d.name,
      code: d.code,
      description: d.description,
      target: e.target,
      weeks: e.weeks
    };
    if (foundInNewData) {
      foundInNewData.values.push(values)
    } else {
      newData.push({
        year: e.year,
        values: [values]
      })
    }
  });
});

And here is the corresponding demo:

const data = [{
    "id": 2,
    "name": "Test activity 51",
    "code": "D51",
    "description": "Description goes here.",
    "years": [{
        "id": 8,
        "year": "2020-2021",
        "target": 65,
        "weeks": [{
            "week_ending": "2020-12-06",
            "hours": 4.0
          },
          {
            "week_ending": "2020-12-06",
            "hours": 2.5
          },
          {
            "week_ending": "2020-10-18",
            "hours": 2.0
          },
          {
            "week_ending": "2020-07-19",
            "hours": 2.0
          }
        ]
      },
      {
        "id": 11,
        "year": "2019-2020",
        "target": 40,
        "weeks": [{
            "week_ending": "2020-01-05",
            "hours": 3.0
          },
          {
            "week_ending": "2019-09-15",
            "hours": 5.5
          },
          {
            "week_ending": "2019-07-14",
            "hours": 1.5
          }
        ]
      },
      {
        "id": 10,
        "year": "2018-2019",
        "target": 40,
        "weeks": [{
          "week_ending": "2018-09-30",
          "hours": 3.0
        }]
      }
    ]
  },
  {
    "id": 3,
    "name": "Test activity 63",
    "code": "D63",
    "description": null,
    "years": [{
        "id": 2,
        "year": "2019-2020",
        "target": 15,
        "weeks": [{
            "week_ending": "2020-05-24",
            "hours": 2.0
          },
          {
            "week_ending": "2020-03-22",
            "hours": 4.0
          },
          {
            "week_ending": "2020-01-26",
            "hours": 5.0
          },
          {
            "week_ending": "2020-01-19",
            "hours": 4.0
          },
          {
            "week_ending": "2019-12-01",
            "hours": 4.5
          },
          {
            "week_ending": "2019-08-25",
            "hours": 2.0
          },
          {
            "week_ending": "2019-07-21",
            "hours": 3.0
          }
        ]
      },
      {
        "id": 9,
        "year": "2018-2019",
        "target": 30,
        "weeks": [{
            "week_ending": "2018-08-19",
            "hours": 3.5
          },
          {
            "week_ending": "2019-02-10",
            "hours": 5.0
          },
          {
            "week_ending": "2018-12-30",
            "hours": 3.0
          },
          {
            "week_ending": "2018-10-21",
            "hours": 2.0
          },
          {
            "week_ending": "2018-08-26",
            "hours": 4.0
          }
        ]
      }
    ]
  },
  {
    "id": 1,
    "name": "Test activity 27",
    "code": "D27",
    "description": "Description goes here.",
    "years": [{
        "id": 4,
        "year": "2019-2020",
        "target": 30,
        "weeks": [{
            "week_ending": "2020-04-05",
            "hours": 2.0
          },
          {
            "week_ending": "2020-03-22",
            "hours": 6.0
          },
          {
            "week_ending": "2020-01-12",
            "hours": 1.0
          }
        ]
      },
      {
        "id": 1,
        "year": "2018-2019",
        "target": 25,
        "weeks": [{
            "week_ending": "2018-11-18",
            "hours": 6.0
          },
          {
            "week_ending": "2018-10-21",
            "hours": 2.0
          },
          {
            "week_ending": "2018-10-07",
            "hours": 6.0
          }
        ]
      }
    ]
  },
  {
    "id": 10,
    "name": "Test activity 59",
    "code": "D59",
    "description": null,
    "years": [{
        "id": 13,
        "year": "2020-2021",
        "target": 15,
        "weeks": [{
            "week_ending": "2021-04-18",
            "hours": 4.0
          },
          {
            "week_ending": "2021-02-28",
            "hours": 2.0
          },
          {
            "week_ending": "2021-02-14",
            "hours": 5.0
          },
          {
            "week_ending": "2020-11-22",
            "hours": 3.0
          },
          {
            "week_ending": "2020-08-16",
            "hours": 2.0
          }
        ]
      },
      {
        "id": 14,
        "year": "2019-2020",
        "target": 18,
        "weeks": [{
            "week_ending": "2019-12-01",
            "hours": 2.0
          },
          {
            "week_ending": "2019-10-27",
            "hours": 9.0
          },
          {
            "week_ending": "2019-09-01",
            "hours": 2.5
          }
        ]
      },
      {
        "id": 12,
        "year": "2018-2019",
        "target": 20,
        "weeks": [{
            "week_ending": "2018-11-11",
            "hours": 4.0
          },
          {
            "week_ending": "2018-08-26",
            "hours": 1.0
          },
          {
            "week_ending": "2018-08-12",
            "hours": 12.0
          }
        ]
      }
    ]
  }
];

const newData = [];

data.forEach(d => {
  d.years.forEach(e => {
    const foundInNewData = newData.find(f => f.year === e.year);
    const values = {
      name: d.name,
      code: d.code,
      description: d.description,
      target: e.target,
      weeks: e.weeks
    };
    if (foundInNewData) {
      foundInNewData.values.push(values)
    } else {
      newData.push({
        year: e.year,
        values: [values]
      })
    }
  });
});

console.log(newData)


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