I don't know what's going on, but the most recent updates have been messing with my save games. It all started earlier this week, when I finished Episode 3 and started on Episode 4. After I exited the game and returned to it later on, my save game had been erased (which wasn't a big deal since I had just finished one episode and was beginning the next)

I started Episode 4 and had since made a good chunk of progress. When I started the game today after noticing it had updated again, the save game I had was reverted to the one I saved when I first started the episode so I lost all the progress I had made previously.

If it helps, I was playing Episode 4 when the update had changed the Apogee screen to the classic version. This last one returned it back to its modern form.

I determined the cause of this problem. One of the updates changed the location it points to when looking for saved games.

Before the update, my saves were stored in AppData\LocalLow\Apogee Software\Crystal Caves HD\Saves but the update corrected it and pointed it to AppData\LocalLow\Apogee Software\Crystal Caves HD\Gog\Saves