This article explains a situation where folders can reappear during rename operations
SureSync supports rename operations that eliminates much of the overhead involved in processing rename actions. In older versions, the files had to be deleted from the old location and copied to the new. This rename functionality is powerful and efficient but you must be aware of some potential issues that can occur if users have files open in the destination folders.
Consider the following example: You are renaming a folder named SalesData to Sales. This folder contains thousands of subfolders and files used by sales employees in multiple offices. If you rename this folder on one side during the business day, odds are good that a user will have a file open on one or more of the other sides of the synchronization. This can result in the folder rename occurring but some files being left behind in the old structure because they are in use by other users. The old folder structure will remain to the extent necessary to hold the files that were open. You will also get the new structure in the renamed location. This can require you to do some additional cleanup later but is necessary to avoid losing someone's work.
To avoid this situation as much as possible, it is recommended to perform renames and moves of large, frequently used directory structures during the off hours when people are not accessing the files. This ensures a clean rename without the need for additional cleanup.