IF both batteries are more or less at the same, non dead, state of charge, then there won't be any damage to the diodes.

If both batteries are very low, then starting and running in "both" will give the alternator a bit of a workout for the time that the switch is set to both. In reality, the alternator is rated for xxx AMPs charge rate and that's pretty much what comes out of it. The current is determined by the difference between the voltage coming out of the alternator and the voltage of the battery (if it were disconnected) at any given time.
Batteries come up out of a low state of charge fairly quickly and as the battery's voltage rises, the rate of charge decreases, so that as the battery becomes more and more charged, it takes longer and longer for charge to get "put" into the battery.

As to how long to run in both.... If depends on the state of the battery, i.e., is it new or on its last legs. If new, then being on "both" for 5 mins or so should be enough to change to then just start on one. IF both batteries are on their last legs , they may never recharge enough for a restart on just one. If I was "at sea" and had to swith to "both" to start and the batteries were more than a couple of years old, I'd probably run home on "both".