It sounds like the root of the problem was not resolved.
First, to address your question. RV's are snowflakes and built differently.
Usually running the engine will charge the house batteries at the same time as the engine batteries, assuming all the components are working correctly.
With shoreline, many later model rv's like yours will charge the engine batteries at the same time.
So you could virtually have two charging sources in parallel. Generally not any issue but you can get some error messages on things that get their little brains a bit fuzzed up.
Sorry about the technical lingo. Fuzzed up means confused!
IF you were having batteries going dead in a few days, I mean two or three, then you either have a drain on them such as leaving a compartment light on or you have a bad battery bank. Often it is bad batteries.
You are starting in a great place to learn about your specific rv setup. Winnebago is one of the best documented ones I have ever owned.
You need to become handy with a voltmeter or a checkbook to sort these things out.
With notepad close, camera there too, take pictures and voltage readings. Print the pictures and write on them. I promise you the measurement you took will be forgotten 30 minutes from now or you will doubt yourself.
Measure the voltage on the battery banks and have someone run the slides in and out.
IF you know how the wire was moved from one battery bank to the other, move it back and see what difference the slide load has on that bank.
I too think you may have some wimpy batteries and the slide will find sick ones quickly due to the heavy load.