I have had a mini breakthrough, though I don't know if my hypothesis is correct. I renamed the folders of the mod with numbers in front of their title, corresponding to the order the FOMOD has the user install them. Ex. "1 Main File," "2 Style," "Choose Texture," etc. I then re saved the FOMOD, tested it, and it worked! I didn't change any file paths, just renamed the folders with numbers in the order the FOMOD should install them. For example, in my initial FOMOD that wasn't working, the texture folder was called "Camo Options," the second folder was called "Main File," and the third folder was called, "Styles." When the FOMOD installed, the main file would be installed first, then you choose a style that overwrites the main file, then you choose a camouflage texture that overwrites the main file. The problem was that meshes in the style folder were overwriting correctly, but texture files from the Camo Options folder weren't overwriting. My hypothesis is that the FOMOD was installing the files not in order that the FOMOD installer had you choose them. But alphanumerically based on the folder names.