Folders with 1 "loose" comic are turning the folders into "single" issue items in JF?

[LivingLitch]

If I 1 single loose comic not in a folder, when JF scans my media it turns that folder into a comic that I cant load. I can have 

Setup
Comic Distributor
-Series 1
--Sub Series 1 Folder - 5 comics, 1 more sub folder
--Sub Series 2 Folder - 8 comics, 2 more sub folders
--Sub Series 3 Folder - 1 comic, 2 more subfolders.

Shows up like
Comic Distributor
-Series 1
--Sub Series 1 Folder - 5 comics, 1 more sub folder
--Sub Series 2 Folder - 8 comics, 2 more sub folders
--Sub Series 3 1 comic - just that one item.

I can "fix" it by going in and tossing that 1 loose comic into its own subfolder but.... I have a lot of comics and lots of folders. I would need to go through every folder and verify that JF is seeing them correctly, then change the structure, then refresh.

Is there a faster way to fix this issue?