We have seen this issue:
When UserA deletes a file in a group sync-ed folder, and if UserB syncs the folder with his local folder, FileManager will prompt UserB that the file has been deleted on server and if it is ok to delete the file on his local machine. If UserB clicks No, then the file is sync-ed back to server, which then propagates to all other sync-ed PCs.
To solve this problem,
(1) You might want to stop sync-ing the folder with all users. You can use the shared folder on server directly. When you need to edit a file and save it back to server, you can simply open the file on server, edit it and save it; the file is saved in a cache folder and then sync-ed back to server automatically.
(2) DriveHQ FileManager has one-way folder synchronization so that it doesn't automatically sync folders from one direction.