We have come accross this a few times now. When renaming a folder or file, they occasionally get duplicated. The only thought we have on this is that there may be another user in the folder or file. Other than trying to get all users out of a specific folder to perform this change, is there another way to do this successfully?
I had my doubst about the point you raised, so I tested your scenario between a Windows & Mac machine. Opened a folder on my Egnyte Drive on my Windows machine. Then accessed the same folder via Mac and renamed it. The rename went through fine. Coming back to the Windows machine and browsing a level back from the renamed folder, I could only see the renamed folder. No duplicates.
Do all your users only use the Desktop App ? Or do you have any who use the Desktop Sync too. If you have audit reports included in your subscription, then I suggest you run a File audit report for the day you renamed the folder which happened to duplicate itself with the old name. This way can know from what access point is the old name getting pushed.
Alternately, you may try to rename the folder from it central location i.e UI and see if that helps you resolve this. Let me know if anything or none of this helps.
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Looking into it more on our end, it happens when a file within the folder is opened through Desktop Sync. It the parent folder happens to be renamed while th file is open and saved, a duplicate folder will be generated.
Is this just one of the downfalls of using the Desktop Sync app?