I’m no expert but I was having the same problem trying to overwrite a file in after effects for a Final Cut Pro project.
I found that if I tabbed away from my FCP project sequence…. over to an empty sequence (or a different sequence) BEFORE trying to render my after effects clips, After effects would let me overwrite the old movie file with the new one.
Then when I went back to FCP I would just tab back to the sequence for my project and the clip would automatically update….just like in the good old days