I like to rename each file in After Effects but when I use the Depencies to collect all files it reverts back to the original name. Which is not helpful if I share the project, how could someone relink if the names of the files are not matching?
You are never actually renaming a source item, just the reference under which it appears in AE. This is perfectly normal. If you want more options, get one of those advanced scripts on AEScripts.com that actually check those things.