This might be a bug report; it depends on whether todays behavior is intended or not(?).
Anyway: if you have properly defined the destination of a file in your application build e.g. on Source File Settings, but then later learn that the file was not actually on the list of source files - adding it to source files will automatically change the destination(!). I suggest it should check whether the user has already defined a valid destination for it and if so keep it.
Here is a demo of the issue:
