The less safe way, and what I do is alter the profile of the backup once every so often for one run to actually delete all the files (advanced setting) in the destination (backup) that are no longer in the source. Then after some time and if you find you no longer need any of the files in the old backup that are not found in the source, and you need the room, you can delete that backup and continue with the new. Starting a new backup from the current data on the system is the safest way to approach a refresh. The program is probably spending an inordinate amount of time cross-referencing and verifying all the files that are in the backup that no longer exist in the source. Every once in a while its a good thing to refresh a backup data base or start a new initial backup.
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