This is an issue often encountered, and for which I’ve answered with workaround suggestions too often.
The vector store search tool, in two different variations currently, directly talks about the files as being uploaded by the user. This hinders the tool, with the symptoms articulated well by you.
A full topic I wrote, besides many other similar issues I could link:
We will see if AMA tomorrow has OpenAI willing to address this, with my question and recommendation (lower in the snippet pictured).