Ah, I understand :) Maybe I should avoid using the skip button too much for this reason. And well, I booted up the game again after I had to close it as the issue didn't seem to resolve after around an hour or so of the game being open. >.<
It does seem that they saved the art from the bad ends I had completed, and they are in the gallery. However, the last save file is from the start of the mage route before I finished all the ends. I had already gotten the good ending in each route and was revisiting them to get all the bad ends. I finished collecting them in the student, mage, and princess route. I'm not sure if this means that my progress was saved or not, but it's definitely not saved in the save files. :/
And nope, it hasn't ruined my experience with the game; it just reminds me that I should make more saves so in case something like this happens. I won't have to backtrack as much. Thank you got your response. ^ ^