I have been having a lot of issues trying to export from Obsidian using the Pandoc Plugin. With Linux I got empty error messages, and with Windows it said that the content was empty.
Turning Internal link processing to Leave unchanged fixed this problem for me.
So I guess that the “empty” error referred to the description of the links.
I couldn’t comment in the post that already asked about this, so I hope it is OK to post this solution here.