Okay, Juhan.
If they are different files but the name is the same, it's understandable that OneDrive has that behaviour. Again, we identify files by their names, so if they have the same, it's just confusion for the device.
Again, and due to the limitations of OneDrive, it's not possible to exclude specific folders from backing up, and all the games have a specific path where they save their save files, so it's impossible to change that route either.
You can however take a look at the solution here, to see if you can exclude .ini files from syncing: https://superuser.com/questions/1568015/exclude...
If it doesn't work, I'd strongly recommend you to stop using OneDrive, and start using Drive for Desktop which allows you to separately choose what folders and files to sync. You can find it here: https://www.google.com/intl/en/drive/download/ . OneDrive just allows you to sync My Documents, Desktop and some other folder, but doesn't let you choose subfolders inside those, so that's a pity.
Let me know how that goes! :)
Note: This is a non-Microsoft website. The page appears to be providing accurate, safe information. Watch out for ads on the site that may advertise products frequently classified as a PUP (Potentially Unwanted Products). Thoroughly research any product advertised on the site before you decide to download and install it. All files have been analysed for malware with VirusTotal, and have shown a positive output, being completely safe to install.