Since my server (running xenial) updated to cups 2.1.3-4ubuntu0.9 last night the CUPS logs have had a considerable number of messages from cupsd stating "Removing document files" - about 3 or 4 a second constantly. Stopping the cups service stops the log-spam, and starting it again immediately resumes it (after a few hundred "Loading from cache..." messages). I've tried removing document files from the cache (there were a couple of ancient ones lying around - it's not a heavily used printer), but this made little difference to the symptoms.
I'm pretty confident this is due to the upgrade as:
1. the spam in the logs starts immediately after CUPS reloads (after the upgrade)
2. looking at the diff for 2.1.3-4ubuntu0.9 it does seem to be fiddling with things related to job clean-up (e.g. cupsdUpdateJobs and cupsdCleanJobs in scheduler/job.c)
If I can provide any further information, do let me know!
For anyone else that encounters this, running "cancel -x -a" to delete everything from the queue (including historical control files) seems to have cured the problem. Sorry for not keeping the evidence around, but I'm afraid after it generated 70Mb of logs in two days I needed to fix it :)