So I've been working on a ROM for about a year, and have put tons of hours into it. I also make consistent backups, so I'm not extremely concerned about this issue, as I can recover my work. However, I am curious as to why (or how) this happened.
I'm not sure what relevant information is needed, so I'll cut to the chase with the problem that has arose.
I'm simply making a new level in my hack; adding new tiles into a level in Lunar Magic, and doing a few overworld tweaks. Saving periodically, and testing in Snes9x also. All is going well, then literally out of no where when I go to test in my emulator (the same way I have been for the past few hours), I have massive graphical glitches everywhere when I enter my levels! Lunar magic displays everything fine. I can add more blocks, view my Map16, save with no warnings, and everything works as usual in Lunar Magic, but it's mangled in my emulator (I tried Snes9x and Bizhawk).
Below is a screenshot of what it looks like in Lunar Magic, and also what the same spot looks like in the emulator:
What it
appears like to me is Lunar Magic suddenly started to ignore... some of my ExGFX files? and defaulted to the original GFX files instead... but retained some ExGFX tiles

The tiles that have been 'replaced' with mangled graphics seem to match up with the locations in the original GFX files. At the time of the glitch occurring, all I was doing was adding more tiles to this snow level; not messing with graphics.
I have tried importing/exporting the ExGFX/GFX files again, and nothing changes in the emulator or Lunar Magic. My game doesn't crash, and I have received no warnings when or since this happened. Opening the ExGFX files in YY-CHR shows no issues, it's only in emulator.
Does anyone know what could have caused this?
If it matters, I have a
lot of stuff in this hack. From ASM patches (~44 minor/major tweaks and additions), ExGFX (~506), plenty of ExAnimation, pixi sprites (~140, mostly disassemblies), UberASM (~62 entries, mostly HDMA), around 2.5 pages of custom GPS blocks, and around 50 full levels + ~50 sub levels. Could I have attempted to cram to much stuff into a 4MB rom and had something overflow? I can provided any and as much detail as needed to help figure this out.
Any help with this matter would be appreciated. I don't want more issues down the line, and I'm only 1.5 worlds away from completion.