Force an Agent deployment on those in Lost&Found, Wake them up then delete them from the L&F folder. On the next AD sync they should show up in the right place (which should correspond to AD OU)
The systems not falling in any tag/criteria is in same domain right ?
you can create a tag (with your domain) for those systems and create a sorting criteria under your domain container, so that the systems will move into that ou and others matching perticular tag/sorting criteria moved to right place.
Let me kknow, if you found helpful or not ?