Ooooh, you added pictures! That's easier for me to understand now I'll go ahead and fix these things now! Thankfully, I haven't merged any layers at all (I have like over 100 layers at the moment....) so these shouldn't be too hard for me to fix.

And yes, haha, I nearly forgot about that serpent... You just reminded me that I need to colour him

THANK YOU ONCE AGAIN.