Every zip file has the version number in it, so if you extracted the game and just made a folder copying the zip file name, that should tell you. The Readme should also have a changelog in it with a version number. If you wanted to be absolutely sure, you could download the newest and copy-paste your save folder over, should work just fine. You probably have the newest one though, 0.4.1 went up in June of last year. Unless you clicked the wrong one by mistake somehow.
Very strange though, because that's exactly what I'm doing. Forgive me for the "dumb" question, but I've gotta ask as part of troubleshooting: are you SURE you're unequipping the clips? They don't have an icon when equipped, just the text, so maybe you were mis-seeing that somehow? Otherwise, you absolutely don't have to do this if you don't have time, but it would be helpful if you could try from an earlier save, see if that changes anything. From the beginning ideally, but if you don't want to replay all that, just a bit further back, maybe at the warehouse battle or something.
I suppose at this point I should ask for the save too. Maybe if I see it myself I'll notice something you don't. Just toss it up on whatever filelocker you prefer, I think Itch should be fine with you linking it.