At least you can modify them manually :-) They are contained in the file .metadata.plugins\org.eclipse.core.runtime.settings\de.innot.avreclipse.core.prefs
To all, this is not the whole truth. The plugin also checks the gcc device list (probably with gcc --target) and enables only this devices which are contained in both lists. It seems, that atmel/microchip "forget" to include the Atmega328pb into this gcc device list even in the 3.61 version, where all the other 328pb files seems to be included (but avr-size still complains about Atmega328pb). My workaround is to use Sloeber with the popolu boards https://files.pololu.com/arduino/package_pololu_index.json,...
I now found my account Informations :-)
Dear Liviu, since I expect to stick on Juno for a longer time because of the formatter...
Thanks for the feedback Liviu, but because of this natsty bug https://bugs.eclipse.org/bugs/show_bug.cgi?id=424453...
In the .cproject file there was an additional entry for a subfolder. After deleting...