I believe you experience much more mechanical failure "risk" by the process of shutting down the motor, switching the battery switch, and then restarting ...
Maybe I'm missing something obvious (it wouldn't be the first time), but why would you need to do this? By "this" I mean: Switch battery use while under way under motor?
When we start from the slip we start in "BOTH." We keep it in "BOTH" until the sails are up and the engine off. That way both batteries get equal charging time--which is only "fair," being as both batteries were used to start the engine.
(forgot yesterday, for example), I switch to "1" or "2." The reason for not leaving it in "BOTH" is to reserve one of the two batteries for starting. Whichever battery upon which we've been running is the one with which we re-start on return, so it
gets all the charging from the engine. Which is only "fair," being as it's been running the instruments and started the engine on its own.
(The above procedure also gives me the opportunity to exercise each battery on its own, so, hopefully, a weakening battery can't hide behind a stronger one.)
In neither scenario do I see the need or sense in switching the battery switch while under way with the iron genny.