Is there a way to remove a deleted file from my backup set without first restoring it?
Under Settings enable backup sets.
Create a set for this folder and one for everything else you backup. For example: 1. Everything excepts logs 2. Logs (/home/user/)
Each backup set has independent settings!! 3. Under Settings -> Backup -> Frequencies and versions You can set the first one to a year. Set the Logs for whatever you want.
When you want to delete logs move the slider down to every day. Wait 24 or 48 hours. Move the slider back to previous setting.