PyCharm on RHEL opening two of same module in debug

I am experienced with PyCharm on Windows. But at my summer internship job I am on a RHEL Linus machine using PyCharm Community 2018.1.

When I debug a module and the IDE stops at a breakpoint, it puts me in a second open version of that module. That is, in the editor the are suddenly two instances of the same file open. I can tell them apart because the paths are different (/proj/dir1/dir2/module.py and /home/repos/proj/dir1/dir2/module.py). When I stop the module from running and edit the file I am in (the /home/ one), then save/close it, the edits are not in the /proj/ version.

How can I make it stop this? (opening that second instance)  Or what should I look into to diagnose the problem? It has started hindering my productivity.