I'm in the same boat as Sidonius. It just doesn't work.
I have Windows 10. I have python 3.8.0 installed, and it recognizes .py files as python files. I downloaded Region Fixer and put it in a folder that's definitely not read-only. I use the "cd" command to point to the directory where region fixer is installed. So CMD reads:
Typing in "regionfixer.py --help" does nothing (though for a brief moment, it seems that cmd is attempting to load something).
Typing "regionfixer.py" followed by a space, and then the directory of the save folder does nothing. Using other directories -- going directly to region\*.mca; trying literally any other directory, etc. -- does nothing. I have tried putting "python" before the command, or the command in quotes. I have tried renaming regionfixer and the folder it is in. I have reinstalled both python and regionfixer multiple times. I have restarted my computer. I have tried placing my minecraft save in a different folder as well. I tried running it through the python command line just for the hell of it.
Nothing is working.
All video tutorials are out of date (the latest one I can find is from 2018), and all of them refer to the .exe version of regionfixer, which isn't available anymore, so the tutorials are useless to me. Your wiki is, and I'm sorry to say this, incredibly unhelpful to those of us who don't have proper knowledge of command lines -- step-by-step instructions detailing everything from start to finish would be an absolute lifesaver for half the people here. I have literally spent three hours banging my head against a brick wall trying to fix my corrupted world -- all other methods I can find either don't work (like swapping level.dat to a new save file) or are out of date (like MCEdit).
Uploading my save is a last resort for me, since the save folder is 5 GB in size (I hand-painted the entire world in WorldPainter, approximately 16x16 kilometers) and I have incredibly slow internet (it could take me at least two hours to upload it). I'd rather do it on my own computer if possible.
I hope this post doesn't come off as snappy or rude, but I'm quite literally at the end of my rope here, and this program could very well save the hundreds of hours I've put into creating this world.
The command line now seems to recognize that regionfixer.py is something that can actually be run, but it still spits out an error:
region_fixer [options] <world-path> <other-world-path> ... <region-files> ...
no such option: Error: No world paths or region files specified! Use --help for a complete list of options.
The error is telling me to use the --help options... which I just did. Again, any other variations of the command I can think of (putting quotes around the file path, typing "python regionfixer.py", etc.) either do nothing, or gives this error.
The fact that CMD is now recognizing regionfixer is giving me a little hope, at least.
Thanks for the honest words. It doesn't sound rude at all and you are right. To tell you the truth, I keep updating regionfixer because has became pretty important in the community and it feels the right thing, but since I played minecraft and coded for fun a lot of time has passed and a lot of things have changed.
I have little free time, and when I have it I prefer to use it to unwind. I have tried to update the windows exe but the library I used has been deprecated since then, the same goes for the GUI. You are right about the wiki, english is not my mother language and, again, I choose not to spend my time in that. If you are finally successful, feel free to create a proper tutorial and I will link to it, or add it to the wiki.
That said, I have no idea what is going on, and I'm really sorry to not be able to help you. As you say that change in ouput from regionfixer seems promising. What triggered that change? What did you do? That seems like a good path to investigate. Please report with any information you have and I will try to help.
To fix this issue, stop the server than try deleting all the files other than obviously server.jar, world or what ever the name of your world is, server.properties and the eula text file than restart the server and you should be able to break stuff and no longer have the issue.
I assume it's usercache.json causing the issue but to be sure deleting and letting it recreate the files is a cleaner answer to make sure.