I created a project ~/PycharmProjects/myproj1 which has module a.py in it.
Then I created a link to this project ~/PycharmProjects/myprojlnk.
I open the latter directory in Pycharm and open a.py.
The crumble path beneath the button bar shows myprojlnk->a.py
Now I set a breakpoint in a.py.
Upon clicking the debug command button (Shift-F9) another tab opens up in the editor with the original a.py file.
The crumble path now shows the absolute path / -> home -> rerens -> PycharmProjects -> myproj1 -> a.py
Unfortunately, this second tab does not show the breakpoint (still visible in the other tab), but it does show the execution point. It halted at the line containing the breakpoint in the other tab.
All in all, this is very confusing and I hope you can improve it.