Yes! All premium plans will sync play positions, played/unplayed status, and series "mark played until this episode" settings across Android, iPhone, and the web app. That means if you play an episode on phone 1 and it's also on phone 2, the file will indeed be deleted from phone 2 according to your download limit and "auto-delete played episodes" settings. It would be just as if you had played it on phone 2.
Essentially, you will always have the same items offline on both phones, assuming they both have the same settings, which is of course up to you. This is generally desired behavior.
You can still choose to keep an episode permanently on your device with a manual download. Also, premium plans introduce a better option for permanent downloads. There are now custom playlists and they come with their own download limit. For example, you could make a "besties" playlist with a download limit of 100 to keep all your favorites offline, even if they're played.