Use Git. You do not need to use GitHub/GitLab/Bitbucket, but doing so will obviously provide even more redundancy for your backups.
If you believe this issue was caused by the PROS Editor, then simply do not use the PROS Editor. That is part of the beauty of PROS — you can use anything from the most sophisticated IDEs to the most basic text editors without being forced to give up integration. I personally greatly dislike and never use Atom (the PROS Editor is nothing more than re-skinned Atom with a few extensions preinstalled), and I have never experienced or heard of an issue like this with any other text editor/IDE I have used.
If you think the issue lies with the PROS CLI (which I highly doubt), then that is a different conversation entirely. But it is important not to label issues as a generic “PROS issue” when in reality the problem could lie with the highly optional PROS Editor or an essential component like the CLI or API.
As for restoration of the corrupted files, assuming (like me) you suspect the PROS Editor to be the problem, your solution (if one exists) will have nothing to do with PROS specifically, but rather the Atom text editor and/or the capabilities of your file system. I recommend searching the internet for a similar issue with Atom as opposed to with PROS, because you will be far more likely to find a recovery (or mitigation) solution by doing so.