From Domino Admin Help:
Because deletion stubs take up disk space, Domino regularly removes deletion stubs that are at least as old as the value specified. It checks for deletion stubs that require removal at 1/3 of the purge interval. For example, assuming the default value, 90 days, when a user opens a database, Domino checks if it has been at least 30 days since it removed deletion stubs, and if so it removes any deletion stubs that are at least 90 days old. The Updall task, which runs by default at 2:00 AM, also removes deletion stubs.
Based on the default 90 day value, this seems to indicate that Domino checks to see if deletions have been purged every 30 days (1/3 of the purge interval), but that it purges only deletions older than the actual value of 90 days.
My understanding was that Domino purges deletion stubs nightly during updall (not necessarily 2:00am) and that it purges deletions stubs older than 1/3 of the value, which would be 30 days.