Is your alternator wired to the A/B switch? If so, I think there might be a problem if you operate the switch while the engine
is running. There will be a moment where the alternator is unloaded, and the alternator output will spike up to a pretty high voltage. This could damage the solar controller.
However, if your two battery banks are a house bank (A) and a starter battery (B), with the alternator wired directly to the starter battery, then there should be no problem.
My boat is wired in a pretty common configuration, where there is an A/B/Both switch, with (A) the big house bank, and (B) the starter battery. My alternator is wired directly to (A), with an echo-charger going from (A) to (B). My solar controller is connected to the main buss (the common side of the A/B switch), although I could have wired it to the (A) house bank (*).
Anyway, as long as your alternator *always* sees a battery load, you should have no problems with smoke.
We've got some actual experts here, so let's stick around and see what they have to say...
(*) -- I have a vulnerability with this connection, where if the A/B switch momentarily disconnects the batteries, then the solar charger
might briefly apply full solar panel voltage to my electronics
. This would be very bad. Fortunately for me, I never use the A/B switch, except to occasionally test that it works.