Not really? You just have to manage stuff as you go. Keep track of every patch or tool you use (including freeram if they require it), and if you run into issues, you just have to look though them for what might cause it. TheBiob is working on a tool to help manage this
, but past that, there is absolutely no way to determine whether a particular patch is intentially modifying one thing or another.
Now, my only suggestion to help solve your issues is to port to a new ROM.
Start with the Lunar Magic-only stuff; "File -> Levels -> Export Multiple" for levels data, overworld editor save for the overworld (same process for credits/title screen), then map16/global pal/exgfx file/global exanimation with their respective import/export buttons.
Then apply main tools (AMK, GPS, Pixi/Giepy/spritetool, etc.). These should have no conflicts if you haven't screwed around with their core ASM files.
Finally, apply your patches/hijacks ONE BY ONE. Key phrase: ONE BY ONE
. Go to where you were encountering issues with each one you apply, and continue doing so until you see the issue start occuring. At that point, just roll back the ROM to the previous version, and now you know where the conflict lies and can fix it.
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