Okay, I unchecked "unless the drive is being emptied" and I manually ran a "re-balance". Didn't seem to work. The files were still there.
However, I went into the rules for those two folders and I switched the overflow setting from 90% to "never allow files to be placed on any other disks" and I ran a re-balance again and it worked! The folder structures are still present on those drives but they don't have any data in them (0 bytes). (Also, as extra info, none of my drives are more than 50% full).
I'm not sure exactly which solution worked but I will say that checking "Never allow files to be placed on any other disks" and unchecking "unless the drive is being emptied" are the last two steps I took before it worked.
Thank you, @Christopher (Drashna) and @Jonibhoni
