When an application is being debugged it is a common action to make an edit in the source when an obvious issue is spotted (often quick cosmetic changes).
It is subsequently possible to hit build and recompile the changes. The debugging instance can easily be left running.
The usual step is then to stop the debugger, and restart with the updated binary.
An extra option (on the "Build & Run / General" tab?) to 'Always stop debugging session on build' would be useful.
This only affects Linux because the running process file can be replaced; Windows would fail to link. However, on Linux, if the debugger is pulled just at the link stage, it causes a bad link.