score:44

Accepted answer

JPA does not limit number of persistence units defined in persistence.xml. This warning just tells about limitation of tool in Eclipse IDE. This is told for example here http://www.eclipse.org/webtools/dali/gettingstarted.php :

Currently Dali only supports one Persistence Unit and one Persistence XML file per project. Other configurations can exist in a JPA project, but the validation and defaults processing may not be correct when multiple persistence units are used.

I guess there is no known way to get this work in Eclipse IDE.

score:33

While this is JPA valid, you may also turn off the resulting (annoying) error notifications on a per-project basis by going into 

Project Properties => JPA => Errors/Warnings

Activate Enable project specific settings and under Type, change the notification level for Class is mapped but is not in a persistence unit from Error to anything else you're comfortable with.

Update for Eclipse Luna:

The location and name of the setting has changed in Luna. The new location is: 

Project Properties => JPA => Errors/Warnings

Check Enable project specific settings

Expand Project group

Change Multiple persistence units defined: to Ignore.

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