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The warning message is from the open source Eclipse Dali JPA tooling. It only supports one persistence unit per project. Here is the related bug:
You can submit an enhancement request to Dali project forum:
Also see Eclipse Dali bug https://bugs.eclipse.org/bugs/show_bug.cgi?id=194833 as this is the enhancement request for Multiple Persistence Unit support.
Also, the reason you are seeing those errors in your first project after generating entities from the second connection is because the project wide schema is being updated to the second connections generation schema. If you go into the JPA project properties you can change it back. This workflow would need to change with multiple persistence unit support.
Use a composite persistence unit with multiple persistence units.