Some textures are stored in the Texturebank folder. Others are stored with the entity in EntityBank. Typically they have a .dds extension, although sometimes .tga, .jpg, or .png. Texture files are usually referenced in .fpe (entity script) and .fps (segment script) files, although occasionally they may be referenced by the mesh (.x) files instead (such as for multi-texture objects). Often the references are to the wrong extension though (such as Texture023.dds may be referenced as Texture023.tga). If the the file with the extension referenced is not found, FPS Creator tries again, replacing the referenced extension with .dds.
When FPS Creator references .fpe or .fps files, it first converts them to .bin files and references those instead. Likewise when it references an .x file, it first converts it to .dbo and references that instead. .dbo files also contain the texture references, not just the meshes. So whenever you update .fpe, fps, or .x files, you'll need to delete their corresponding .bin and .dbo files (it shouldn't do any harm to delete all .bin or .dbo files at any time, FPS Creator will just create new ones as needed). .fpe and .fps files can be modified with a text editor.
A given texture file can be referenced by multiple .fpe and .fps files though, so when you move a specific file, you'll need to find and update all references to that file. If you really want to reorganize the layout of what's in the FIles folder, you may want to create a backup of it first.
Judging what we see is the greatest blinder and self-limiter in the universe.
What we perceive is never reality. It is only a story we tell ourselves based on our current perspective, which has far more to do with our beliefs about ourselves than with anything else.