This shouldn't be the case. The game can automatically load a save file from a previous version.
However, if it's the other way around, where you play a previous version game with a save file from a future version, then there's a huge chance the file will reset.
You might find a "NudeByte.sav" file in the new version game folder. If there is one, it's a backup file of your save data from the previous version.
If this is the case, you can download the Save Transfer software above, copy this "NudeByte.sav" file and paste it inside the Save Transfer's folder, run the Save Transfer, and import it. Hopefully, this will help you get your save data before the reset.