Unfortunately we only push data at this time and do not monitor the state of the updates distributed to locations within a Distribution Center. Thus you are correct in that if you were to delete the Distribution Center Location contents manually, LUA would not be able to re-sync this data.
LUA when it pushes out replacement updates, does not remove the replaced updates automatically. We have got a setting that will allow LUA to purge extraneous updates at a location. Can you confirm that you have configured through Configure > Preferences a setting "Purge updates in Distribution Centers " that will purge the data?
We would like in the future to introduce additional features...
- location administration tools that, as an example, would allow you to take a location off line for maintenance
- intelligent monitoring that, as an example, would monitor the state of content in each location and take appropriate actions when required to keep the location in sync. An additional item here would be the ability to forcibly sync a Distribution Center Location