According to how the disconnect switches are wired, you can't be sure they will charge with switches set to off. You can test though:
To check if all batteries will charge, use a multimeter on the batteries after they've been resting a few hours. (This allows 'surface charge' to be absorbed)
Then plug in to shore power and test each battery again. You should find an increase in voltage at each battery if under charge. You could repeat same exercise with engine started to be sure they all charge on alternator too.
Question is, why not use the on board generator to charge batteries, and exercise generator at the same time? It will require a couple of hours of run time.
Battery disconnect switches often don't completely disconnect batteries from phantom charges. On my RV, the chassis BDS is 100%, but the house BDS isn't and will allow batteries to go flat. I have knife switches on the house batteries and they then are 100% disconnected. I left it in storage for over 3 months this winter while we were out of the country. When we returned, I started engine and generator with no issues.