I think I found the issue. The index is still rebuilding, but it's looking good.
$is_enable_external_links was not being set to true when calling GetCachedFileContent_ByLocalLink
Below are the changes I made in wpfts-add-on-for-wp-download-manager.php
This may or may not be the correct way to fix it, but, as I said, it is looking good. FWIW, There is another area in code that appears to have the same issue, bit it's for different versions of WPFTS, so it won't affect me.
I'll post an update tomorrow after the rebuild finishes to confirm whether or not this fix worked.