Switching Between Episodes in LS3
I believe when you complete a section of any of the stories after Season 1 (ie. Seasons 2+3, plus Heart of Thorns), you can switch to another story with minimal loss in story progress. I recently had a character switch his active story from S2C7 to S2C1 and although it warned me I might lose progress in C7, I think it just means I’d restart from where I ended. However, to play it safe, I suggest you do one of the following:
1. Just finish the chapter. Season 3 chapters are repeatable, so if you want to play it again, you can do so once it’s complete.
2. Take one of your other characters and have them do S3C2. There is no prerequisite to running a chapter besides having that chapter unlocked, and being level 80. So if your intention is to get all your characters to Ember Bay, just take that one down there first and have them buy the portal map.