See Backup your iTunes for Windows library with SyncToy. If a sync upsets something in your library you can restore the previous version of the database, export the playlist, sync again, and then import your list, and sync one more time to get the correct version on the phone.
Or, if you know that you've messed up a list on the device, then you can backup that list before you sync for the first time, but you should be maintaining a backup anyway.
I haven't tested it, but it might be the case that if you deselect a playlist for syncing before you start then any changes on the device won't be copied back into the library. You could then sync the correct version on a second sync. This is probably the closest to what you want, if it works.
Another possibility is to right-click on the playlist in the side bar and duplicate the list before you sync, deselect the old list for syncing, select the new one to sync, sync, then remove the old version of the list from your library, rename the new one, and sync again.
tt2