Yeah, it really sucks because the whole point of having a skip button is to help save time, but if it breaks the game, it's kind of a pointless function >.<
The way Tyranobuilder works by default is that all images like CGs, once viewed, will unlock in the gallery even if the game isn't saved, so that's why those are still there. It's so that you can start a new game and stuff without losing any gallery progress :3
But yeah, the endings that you got won't have saved like the CGs have >.< because they're tied to the save files instead. So for example, if you were to go back through one of the routes and just go for the good ending, the game won't recognise that you got any of the bad endings for unlocking the ??? route before the game froze >.< It'll only count the ones from your last save, unfortunately :( So you'll have the CGs, but not the actual bad ending points that count towards unlocking the route.
That makes it even harder to know which ones you've got and which ones you haven't >.< There is a loophole that I left in the game though for getting easy bad ends if you need to exploit that for unlocking the ??? route without actually having to go through all of the bad endings again :3
I'm still sorry you've experienced such an annoying problem with the game anyhow >.<