Update: I figured it out! It seems to be some sort of conflict with another export extension I sometimes use GMLink
https://pr0te.itch.io/gm-link
Disabling GMLink and restarting Aseprite fixed it, still no permissions pop up, but I guess the old permission I set ages ago maybe worked once GMLink wasn't running?
Turning GMLink back on causes the error to re-appear so looks like that's definitely the culprit.