HDD folder does not show files but I can still transfer files

[ghisler(Author)]

I see - can you try to upload the files to a different folder, and rename them BEFORE uploading them?
You could use the multi-rename tool in Total Commander to rename the local files, upload them to the disk, and then rename them back in the multi rename tool via "undo". You need Total Commander 3.0 beta to use the multi-rename tool:
https://play.google.com/apps/testing/com.ghisler.android.TotalCommander