Thanks for the responses. That is reassuring to hear.
I've managed to test on a large replica and confirm that the replication history is maintained, as such doesn't require a one-time replication following completion.
Update - 30/10/2014
While initial testing showed that the replication history table was maintained, use of this command does force all users to do a full one-time only replication after the compact completes. This is something to be very wary of as the impacts for users can be significant for large databases with high document counts.