I’m sorry about your java source file being overridden by the Projucer. The Projucer’s behaviour of wiping any files that is in the Builds sub-directory is a common pain point for JUCE new-comers (this doesn’t happen only on Android - but with any exporter) and we are thinking about ways for the Projucer to warn users when it detects that the user has made changes to files inside the Builds folder.
However, JUCE does support you using your own activity class although it is a bit cumbersome and also may change in later JUCE versions. Basically, you need to create a separate Activity class (in separate java file) which inherits from JUCE’s activity class. You can then specify your custom activity class in the Projucer:
To make life a bit easier, the Projucer will not wipe any Java files in the Build folder which the Projucer did not create, so you can put your sub-class next to JUCE’s java activity source file.