It's actually because the public version is earlier, so it might not support elements from saves in later versions. In general, you shouldn't take saves backwards in version from their current state (I might even save the version on the save file and let the user know if a save file is outdated).
Viewing post in Save File Corruption and Overwritten/Modified in v0.3.10.4
Oh, you're right, it is an earlier version... I see, I thought even though it had been nearly 2 weeks, that the free version of the game would be more up-to-date. Either way, I would have a strong preference for it to not nuke the save and instead just render it 'unusable' (I.E. an error message saying "This save is incompatible") In the previous case, I used the free version after using the Patreon exclusive version because I figured it was newer, and I ran into the same issue. Saving version information would be very helpful, and having the game recognize this version mismatch as well would be great.