Yeah, sorry 'bout that. All maps are stored in the "Caches" directory which doesn't get backed up. So far, with major OS upgrades, Apple does a backup/update/restore. So maps and ERSA/DAP/AIP gone.
The good news is: this should be the last time as updates from iOS 5 should now be incremental, without requiring iTunes.
There is one complicating factor: there is no file-system location right now that is both not backed up but also guaranteed to not be emptied out. Technically, when disk space is getting low, iOS could start emptying application specific cache directories.
At the same time, stuff like our maps are not allowed to be store in "Documents" anymore because of long back up times to the new iCloud service. They check and will reject apps for it.
Rock, hard place.
We (and many other app makers) are going to petition Apple to create a new directory, call it "PermaCaches" - not backed up, not removed by the OS either.
In the mean time, always keep a GB or so free on your iDevice to make sure iOS cache cleaner doesn't clobber the biggest "offender".
Bas.