I move my battery switch from 1 to BOTH to 2 and vice-versa with the engine running all the time. As long as it's a make-before-break switch (and I have never seen one that's not), it's fine.
I run mine one either 1 or 2 99% of the time just because I alternate between the two batteries one full day at a time, but it's no big deal to run it on BOTH and it will not harm the alternator to do that. My truck operates with two batteries all the time, there's no switch. Two batteries in parallel is just one big battery to the alternator.
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