Delete files from rdiff-backup
The process for dealing with deletions when you've run out of space is described in the unofficial FAQ under How do I remove files from the backup set. Repeating here just for completeness.
This method is very dangerous and shouldn't be used, unless the files that you want to remove are causing your backup drive to run out of space and your only alternative to removing those files is removing entire increments.
IMPORTANT: Properly speaking, you should do step 4 for every increment of mirror_metadata. Rdiff-backup prior to 1.1.1 does not mind having extra mirror_metadata entries for files that are removed from the backup set this way, except in the most recent version of mirror_metadata. However, at 1.1.1 the mirror_metadata handling changed -- rdiff-backup now diffs the metadata files -- and it's unknown whether having extra entries in these diff'd files will affect restore operations. (Technical note: the mirror_metadata diffs are NOT using the same method as file diffs. They are not rdiff delta files, but plain text files (and no, they are not ordinary text diffs either). Because of this, it is safe to hand-edit them, so if you need to you can do step 4 on these diffs.)
Check the time -- make sure it is not close to time for a scheduled run of rdiff-backup. Also make sure rdiff-backup is not running.
Go into your mirror target directory and delete the file or directory there.
Go into rdiff-backup-data/increments on the target and delete all traces of the file/directory there. Important! If you are removing a directory, make sure you find and remove all of the *.dir files for it as well! If it's a file, make sure you find and remove all of the *.missing files (if there are any). Be careful not to remove anything that isn't related to the thing you're trying to remove, or you might lose the ability to restore other files.
Important step! (and WARNING this is untested with rdiff-backup 1.1.1 or later) Go back up into rdiff-backup-data and gunzip the latest mirror-metadata file. Edit the mirror_metadata file in a well-behaved text editor (WARNING! Do not use pico or nano or anything else that might automatically do line wrapping!) and remove all references to the file or directory you deleted. Be very careful not to mess up the format of the file.
it appears somebody made a script doing the above steps https://www.eugenemakerspace.com/wiki/Sites/Rdiff-backup-delete
I didn't test it, but choose a 'saver' way by deleting all files which are already gone voor 2 weeks, by running
rdiff-backup --remove-older-than 2W host.net::/remote-dir
more example http://www.nongnu.org/rdiff-backup/examples.html
The official github repository for rdiff-backup now has a script to do this:
The script referenced in the other answers does not seem to be available any more.