Also interestingly enough..
if we delete the non _ folder, then everything works fine and it actually recreates the non _ folder again. If we delete the _ folder, things don't fix... it's only when we delete the folder that doesn't contain the underscore and then access a webpage for it to be recreated is our shop fine again... so based on this information, it likely doesn't have anything to do with both folders being created, just a conflict in the non _ folder.
Why is this so complicated?