Can't figure out why stage hack is freezing.

[Nucleotyde]

I've been trying to work on some stages lately, and I'm getting some odd freezes that I can't figure out. Sometimes when I go to test my stages, they'll freeze on selection (no beep and I'm in PM) even though the .rels are correct and they are under the correct filesize. I've been making these stages piecemeal from other stages, and the crashes seem to have something to do with deleting or importing certain files, but I can't figure out exactly what the problem is. Any ideas?

Edit: I should probably mention the files, but I've been working across a few stages and have been having the same problem with all of them. Sometimes it's after deleting a BRRES, or deleting a model from a BRRES, or replacing a COL with one from another stage. Since it's been happening after deleting different files, and doesn't always happen after deleting these types of files, I'm confused about what exactly I'm not supposed to touch.