You didn't answer me, regarding whether was it SAV edits or ROM edits. (my first line in the previous post)
If it's ROM edits, the mon in the den shouldn't change. The only explanation would be you messed up your hacking, or the server now patched the missingno raids.
If it's SAV edits:
If it's just changing the raid seed, well that wouldn't cause missingo raids. (this is the first time you brought up missingno raids, FYI. I was working with incomplete information)
If it's modifying the dai_encount/normal_encount, well you wouldn't be able to bring missingno raids online at the first place...
In any case, there isn't a "solution", because what you are doing is going against how the servers presumably work.