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 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. ðŸ˜
Series that weren't synced were left untouched. iTunes still records 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. 😕
I'll file a bug report later, but in the meantime 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. Restore a copy of the pre-upgrade library from the Previous iTunes Libraries folder.
3. Rename the current .itl file with the suffix (BAD), then move it into the Previous iTunes Libraries folder.
4. Remove the trailing date from the library file restored in step 2.
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.
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.
tt2