When a folder is deleted from one path of a synchronization, that folder may not always be deleted from every other path. This can occur if the "File Masks" specified for the Rule exclude replication of a file that is contained in the folder in other paths.
For example, if your File Mask specifies an entry for "-*.tmp" and some copies of a folder contain ".tmp" files, when you delete one folder, the others cannot be deleted because they are not yet empty. Since ".tmp" files are excluded from the Rule, they cannot be deleted leaving a non-empty folder. SureSync will not delete the non-empty folder. You must change the File Masks or manually delete the folder in this situation. If you do not, it will reappear on the next successful run of the Job.