IPhone – Certain podcasts not syncing to iPhone when subscribed through iTunes

This has been bugging me for years, most specifically with This American Life and To The Best of Our Knowledge.

The tag that's causing them to be separated is not available via iTunes -- you need an extended tag editor. On the Mac, I used ID3 Editor.

Instructions specifically for ID3 editor:

• Open a "good" podcast file (you can drag it straight from iTunes onto the ID3 Editor icon in the dock to open).

• Click on the Podcast tab. Look for the field called Feed (It may have a different name if you're using different tag editing software). Copy the Feed field contents.

• Open your "bad" podcast files, paste/replace the "good" Feed info into the Feed field (they should be different - mine were) and click Update.

• Last important step is that you have to delete the "bad" files from iTunes and reimport them. If you right click or control click the file in iTunes before deleting, and select "Show in Finder," the enclosing folder will open. If you sort by date modified, all the podcast you just updated should be at the top, if they're in the same folder. Then you can delete all the bad ones, and drag them back into iTunes. Whey they're re-imported, they should now be grouped with the "good" podcast.

This IS actually the case.

What you should have a look at is the selection option that you have set.

For instance, if you ask to only sync the "3 most recent unplayed episodes", it might be that the one you are listening to will be replace on your iPhone by the newly released episodes that have been downloaded in iTunes. When the episode you haven't finished will be one of the 3 candidates to be synced (i.e. "when you have listened to all the newer episodes"), the listening will continue where you were the last time you listen to it.

EDIT after the EDIT of the Question :

Hm, ok, with this edit my answer is not right anymore BUT i think you should have a way have it work as you want. If you select for instance "the oldest unread", the one you are listening to will be kept on the iPhone (if you listen to the episodes in order that they are realeased) Another trick is to use the checkboxes on the left of each episode and set the preference to "Sync only checked"