Are you using the sync features in iTunes between devices? Do you have iTunes in the Cloud enabled? I have none of the Store/device sync settings enabled nor use iTunes in the Cloud nor use the iPhone app and I experience no deletions of old podcasts, and I have plenty of them.
It seems there are issues when using the iPhone app with iTunes and enabling the sync podcast settings in iTunes. Correct me if I am wrong. How are you managing your podcasts?
I should consider myself lucky to not have experienced any of the podcast issues with iTunes 11.1.1 (I skipped 11.1). I read some of the other posts regarding the auto deletions of old podcasts and figured it might be related to the "sync podcast subscriptions and settings across all devices" setting in iTunes. I am not certain though as I have never set up to auto sync any iPhones, iPads or iPods with iTunes on a computer.
I have always manually managed iTunes and iPods and used 3rd party software and Applescripts to sync certain settings, as my library is huge and I wanted to avoid any accidental deletions. I have a lot of old podcasts that I have also managed manually, none of them were deleted or disappeared. Call me old school, but I don't like any automation when it comes to managing my precious music files.
Apple made significant changes to syncing podcasts without making the users aware of the consequences. When you first startup iTunes the preference to sync all devices is checked by default which then runs its course. Bad idea. There is also no detailed instructions or info available on how to set up the syncing of podcasts between multiple devices as far as I know.