Not sure if this helps ... but throwing my experience in here. I am getting sporadic episodes skipped when I try to sync from iTunes to my iPhone 7 plus. like I have first, third, seventh etc ... skipping a lot of episodes. I tried to resync after verifying that my episodes are manually set to "Not Played" ... and setting say "download all unplayed". Still no good.
This worked though ...
with device not connected ... in iTunes only. Select all episodes, and select Get Info, and edit to change media type to "Music". It will now show up as an Album in your music. Connect the device and sync. Next, disconnect device and select all the "songs" in the album in iTunes, right click, and select Get Info, again, and toggle in OPTIONS from music to Podcast. Sync again. All episodes of the podcast that are in iTunes will go to the device.
Sometimes, this needs a few rounds for me ...
I will offer this about my situation. I created my own podcast from mp3 files ... they are teaching episodes that have 100 or more "episodes" ... not songs. I want them as PODCAST so that I can rewind 15 seconds and re-listen again to catch complicated things being taught in the course. I also do not want them deleted, once listened to, from my phone. I re-listen to them multiple times before I manually delete them from my podcast.
And this ...
I like id3edcmd works great to wrap perl scripts to quickly edit things like track x of X in the mp3 files, or change the title, or change the cover design (although I know you can do that in iTunes as well).
Hope this helped ... Let me know too, I'm interested.