the LLM's can't tell the difference between two files if they are named the same.
i think the issue is not in the LLM but in the way the research module works.
seems to be a reoccuring and easily reproducible issue. (at least for me)
i mainly come across this when debugging code, i'll upload a file to it, it'll suggest some changes,
i'll make the changes in my editor, save, reupload, ask it more questions, and it'll accuse me, saying the reason i am encountering the same issue is because i never made the changes, when i did!
i can work around this by appending number i increment each time to the end of the filename before i upload, but as i'm sure you can understand, that's sub-optimal.
to test it i gave it two files named the same but with significant differences in the contents, asked it to diff them, and it says they're identical when they're definitely not.
here's a link to the damning thread
https://kagi.com/assistant/cdd96cf3-9a86-425a-82e3-342135acc144