I was going to link directly to one of my earlier posts like this, but I've added in just a little more information...
I'm fairly sure the reason for this is a due to a mismatch between options to Keep all episodes in iTunes and Keep all unplayed or some similar option on your device when the new option (introduced in iTunes 11.1) to Sync podcast subscriptions, settings and stations has been enabled. I lost all played episodes of all podcast series that I synced to my devices. 😠
Series that weren't synced were left untouched. iTunes still recorded both my default option and series specific options to Keep all episodes. iTunes doesn't manage my media folders. The deleted episodes were not sent to the recycle bin. Some people have said they found some episodes there so check.
Here is the recovery process, assuming you have a backup of the deleted files...
1. Restore copies of all the deleted podcasts to the Podcasts folders from your backup.
2. Rename the current .itl file with the suffix (BAD), then move it into the Previous iTunes Libraries folder.
3. Restore a copy of the pre-upgrade library from your backup or the Previous iTunes Libraries folder.
4. If necessary, remove the trailing date from the library file restored in step 3.
5. Start iTunes, go to the Podcasts section.
6. Uncheck the option to Sync podcast subscriptions, settings and stations then click Continue. This should prevent a repeat of the deletions.
If the above screen doesn't show go to Edit >Preferences > Store and uncheck Sync podcast subscriptions, settings and stations.
7. On your devices you may also want to change the Episodes to keep to All in Settings > Podcasts and then again with the settings for each subscription in the app.
8. If, like me, you updated a whole bunch of apps before realizing there was a problem, you may find the restored library has multiple broken links to any apps that you updated. Use File > Add Folder to Library and select your Mobile Applications folder. Accept the offer to replace older versions with the files you are adding. iTunes may prompt that certain files cannot be updated because it can't find the file to add. Keep a note of these as it looks like this happens when both the old & new versions would be given the same file name and iTunes unhelpfully erases the file that it is supposed to add. You can delete any remaining broken entries, close iTunes, then reopen and download from iTunes Store > Purchased > Apps > Not on this computer.
If you don't have the episodes to restore then at least visit iTunes > Preferences > Store and Uncheck the option to Sync podcast subscriptions, settings and stations before attempting to redownload any older episodes.
If you've lost episodes that cannot be redownloaded, and you've not done too much with the drive since, then an undelete tool might recover most of them. FreeRecover looks promising, Select the drive, use the options to get file paths and check file integrity, then, presumably, you can restore anything that has been deleted from the podcasts folder that has a good integrity score. The free version of Recuva might also work.
tt2