I had a look back at the post I was thinking of, and I think the issue with the note links was actually and issue with the import rather than the export. The screenshots show that the note links were correctly substituted to relative paths, and the OP reported that the import did report an error but still did stuff. So I guess the issue is the import process stopped before it reached the logic to convert the relative paths back into links by ids (resource paths were also not working).
The first attempt resulted in a subdirectory that cannot be copied or deleted
This suggests that the import failure was caused by a too long file path. Seeming as the export was successful, it suggests there is a shorter file path constraint for the import vs the export