Does "Remove Permissions" affect the entire site collection?

I have a list a with a lot of user entries in the permissions. There's so many that when i try to modify the permissions, it slows down my farm. I thought i could run a job to remove the user entries from the list but when i looked at it, there's a note that says "Note: This can affect all sites within a site collection." So then i didn't run the job on the list because i was scared! I don't want to change anything for any lists except the one I selected! Has anyone run this "Remove Permissions" job and ran into issues?