If you pause the LQE data sources, LQE will stop receiving updated data from the applications.  When you unpause the data source, LQE will start indexing again where it left off - so, it will begin processing the changes from the applications that happened while the data source was paused.  Depending on how long the data source was paused for, there may be a large number of updates that need to be processed; so it could take some time for LQE to "catch up" again.