If you have the Windows version but also played the Linux version while Cloud Sync was not working then, because cross-platform Cloud Sync is now working, I imagine it could be possible that the few new saves you made on your Linux version could possibly (probably not) overwrite all your Windows saves.
IF YOU'VE PLAYED TAXINAUT ON BOTH WINDOWS AND LINUX THEN I RECOMMEND YOU BACKUP YOUR WINDOWS SAVES BEFORE STARTING TAXINAUT EITHER ON WINDOWS OR LINUX AGAIN.
I'm 99% sure there's no problem but I'm not 100%.
Note: If you haven't played the Linux version yet or don't care about your old saves (since you have to start a new game anyway and aren't going to import your old character) then this doesn't matter of course and everything will work just fine.