Currently, versioning in Proton Drive appears to depend on changes to file size (this is what I have been told by Proton support when I noted that certain files were not being versioned.) If a change to a file doesn't change its file size, Proton Drive won't create a version history for it.

It would be better (and make more logical sense) to have versioning occur if the modified date for the file changes, since that by definition would mean that the file has been, well, modified, and so the old version should be saved.