Hey Dan,
There's no way to deactivate "manually activated" systems. Deactivation requires an internet connection (as does the IsGenuine -- so there's no way to re-validate manually activated systems either) because the server needs to confirm the deactivation actually took place.
If you need to activate additional computers either deactivate the user within LimeLM (which doesn't deactivate the user's computer - so they can still use the activate software uninhibited) or increase the number of allowed activations for the product key.
Does this make sense?