Sync is unstable

I have two Windows computers where I manage to do my work. One is an Laptop, the other is an desktop.

I have left my laptop "B" by like, ~3 weeks, and after that, it loaded filen and "did the sync".

I expected that it would download new files and delete deleted files from the desktop "A", but instead, it uploaded all changes from the laptop "B" to cloud and the computer "A" synced it, downloading old files and adding removed stuff.

I could recover some files in the trash, but the thing is: after recovering files from trash, it didnt go to the original directory where the file was, instead, it got in the root directory. Now I have more than 300 files mixed with my folders in the root directory.

Now it's a complete syncing mess. Already tried OneDrive, Mega Sync, Proton Drive, Syncthing and now trying filen.io and my conclusion is that no syncing service is really good that I can trust it will work correctly.

My only choice now is to recover important stuff (happily I have latest stuff on git repositories), but now I need to delete the remote directory where I was doing the sync and redo the sync again.