That's odd. I'll look into it, thanks.
There's no risk of losing saved tracks between itchio and steam.
Unless you've put the itchio version inside your Steam folder for some reason, they'll be completely separate. Just find the save folders:
- Steam: X:\Program Files (x86)\Steam\steamapps\common\Tracks - The Train Set Game\TrainSet\Saved\SaveGames
- Itchio: [Download location]\TrainSet\Saved\SaveGames\
And you can copy/paste the saved tracks between the versions. You could copy that folder to your desktop to have as a backup too if you want to be extra safe.
(the UnlockProgression save game keeps track of which items you have unlocked so you may want to copy that over too)