How to remove stale, orphan folders from the Box Drive folder?

I am using two Windows 10 machines which share my Box account, and regularly use Box to transfer files between the machines. The problem is that on one machine I have a few directories which were removed using the other one.

Looking at he online account, I can see that those folders were removed. However, they are still present in the first machine, have a red-dot status and constantly attempt to sync, which slows down the computer noticeably.

When looking in Windows Explorer, these folders look empty. Their properties show 0 files inside. Yet, I cannot delete the folders. I tried deleting from Windows Explorer, as well as form the Cygwin Bash terminal command line and from Windows CMD command line.

When trying to "dir" and "ls" the folders, it says they are empty, but when deleting using "rmdir /s" or "rm -rf" (and other methods) I get an error saying that the directory is not empty.

It looks like something on the first computer is out of sync with Box. How can I permanently remove those folders?

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