What happened was that, when you deleted the files on your laptop, your hard disk's back-up software updated the copy on itself to match what was on your hard disk.
There's most likely an option within the back-up software to control this. Check the manual and/or the help of the backup manager. If you still insist on deleting the backup program that came with your drive, you can just back it up to another location in case you want to use it again.
WDsync automatically copied or mirrored your current Desktop files to the passport thus you should turn off the auto-update feature. You dont need to delete the WDsync software entirely because you might want to use it someday so you can create a new folder and just stash all the WDsync fliles inside it and turn autosync off.
I did this and I just back up my files by either manually opening the Sync program or just copying the files old school way. Either way, you lost your documents because the Passport copied the current state of you desktop.