It is pretty common to miss a bit when we think we see something! I feel the brake pedal is not involved in the coach/chassis charging question as it is just a gizomo that should work automatic but seemed to do different after brake changes.
Gremlins have a way of trying to fool and I think the timing some way threw you off as there is no connecttion to the brake on these parts.
I might throw in some ideas on what you can do to try to sort the question OR in a bad case get the two jumpered together.
This is the drawing set which is involved with that section. We used to get a "mode solenoid" and it was a bit of trouble as the contacts arced and burned way too soon/ too often! Now we get a "battery isolation manager" that connect chassis and coach at the right times.
https://www.winnebago.com/Files/File.../000164549.pdf
So they now use solid state gizmos which last longer but we can't see/hear them work, so we have to do more testing!
Click these snips to get a better view or go direct for the whole story?
Under the passenger seat you should find this area?
Note the disconnect relay that the switch operates when we push the battery disconnect switch. But the thing you need to find is kind of hidden to the left out of sight on this drawing!
This is the BIM and how it should work!
You should have a big cable from the coach batteries that I marked in red on one big post of the BIM and a second calble going tot he disconnect relay. If that relay is closed to let power through, it should pass on through to a cable going to the generator starter solenoid to start it!
So you have at least those three connections to check and make sure they are clean and making good contact for the generator. Dirt is much more a problem than the relay failing so I look for the simple things first!
But when we push the boost switch or when we start the engine, there is ground on wire FM and 12volt on wire LR (blue marked wires?) to make the Bim connect cables I marked red and green together! Like the mode solenoids but solid state gizmos!
So if you find the coach batteries are not connecting to the chassis battery to charge, etc. this BIM is a place to check.
Before tearing the seat out, etc to get to things, I suggest doing a check first!
When it has all been shut down for a few hours, the two battery, coach and chassis, normally will be a bit different voltage.
If you note that voltage on each, then start the RV engine, you should see the chassis battery dip pretty big while cranking but then as the alternator starts working, that voltage will jump high. Maybe up to near 14 if you rev the engine?
Then check the coach battery and you should see near the same voltage as you rev up the engine---assuming the BIM is doing it's thing right!
OR When the engine is NOT running, if you watch the voltages on both battery sets, they should jump up and match pretty close if somebody is pushing the dash switch to connect them!
You "may" have something broken but the most common problem is dirt and corrosion on the cables, so you may have to chase the cable all the way back to the generator and where it connects there.
But if you REALLY are in trouble, one way to jumper around a bad BIM or such is to jumper across the two big lugs on it!
Some what simple but those gremlins do sneaky things!!