I might be mis-interpreting your complaint here, but I suggest looking at the bullet point above the set symbols in the Setup instructions - it should list the required encounter sets by name there.

Did they advise which random other channel they're moving it to, as well?

I'm not sure on the etymology, but is "Indgredients" period-appropriate, or just a repeated typo?

I'm impressed - they hit 11 on my Underwhelmed dial.

It should say during the relevant resolution whether or not you keep an Ally that you encounter during a scenario, and who may end up with them - it'll either specify the lead investigator gets to add X, or that any investigator may add X to their deck, ignoring restrictions.

Playing through both halves of The Dream Eaters at present - completed the first scenario for each side, though we ran out of time to do the first interlude on Friday night, due to sheer volume of flavour text. In campaign A, I'm running Akachi, alongside Tony, Preston and Mandy In campaign B, I'm running Patrice, alongside Dexter, Trish and Tommy - Dexter nearly had problems in a Staircase during the scenario, and it took some careful play to ensure he didn't get killed (multiple infestation tests in one turn meant he gained three enemies, including a 3-strong Swarm - which a DoN Improvised Weapon from Patrice took out. I maintain it was a copy of The Sunday Times, with all the supplements). Looking forwards to my next XP spend with Patrice - I've played her at 9XP for Arkham Nights and other one-offs before now, but not at 0XP (oh, how I missed Cornered at times), nor with more XP available, so upgrading should be interesting from here on out.

I think I saw one in one of the scenarios for TFA, but that was also combined with removing some other tokens, which may be slightly different.

FFG, you really need to look at how many of these you are producing in a wave. Sheesh.

I've taken a look at the specific wording in the Innsmouth campaign guide, along with the rules reference, and I can't see anything that would explicitly direct you to remove them. If I hadn't seen this thread, I think my default response would've been that they get left in, just like any other change that is made to the Chaos bag due to scenario intro/outro effects.

Sounds like a given for the FAQ/errata document, if it currently isn't clear.

...the common cold?

The solution is still kill all of the cultists... right? Paging Zoe... Murderbot required in aisle one...