Already tried this. Retried and it didn't work. The .sav did not create the freezing, but the .sav is most certainly freezing.
I'm not 100% that the backup is the original, and unfortunately I did not create my own backup. The problem is not in pokegen, I'm guessing the .sav has some sort of corruption. Creating an entirely new .sav off of Pokesav still produces the same error.
EDIT: Was able to open a save file off of the .sav where I had deleted the Conkeldurr, and miraculously was able to save this instance of the game save (but only if I immediately left the area. If I walked into a trainer or started a random encounter the save would still crash. After leaving the area, I could reenter the desert area and play normally. The only exception was a ????????? pokemon where Conkel previously was. I saved the state immediately after leaving the area, and decided to play around with this mystery pokemon. I could swap it's position in the party as well as giving it items. In a Pokemon battle in the switch Pokemon interface, I could hover over it's frame in slot 5 but was not able to interact or choose it. Swapping it into the front of the party and initiating an encounter crashed the game. The pokemon could not be deposited into storage, even if it was holding an item.).
To fix the problem, I edited the ?????? pokemon out with pokesav and replaced it with my original Conkeldurr, down to the stat. I'm sure PokeGen would have accomplished the job just as well. I am incredibly relieved to have my eight and a half hour save file back in playable condition. Thanks for your replies and your time.