If your batteries are dissimilarly discharged during flight (which is
possibly the reason you want to switch batteries) then the instantaneous
current flowing through your circuit when you join them could be quite high
and cause you more problems.

There are two better ways to solve this problem:

1) Insert a capacitor across the power as has been suggested. A further
enhancement would be a choke across the switch.

2) Power your loggers etc off a separate bus which is connected through a
rectifier bridge to both batteries. The logger will draw power from the
higher voltage battery and neither battery can charge the other. There will
be a voltage drop of between 0.5 and 1 volt but most loggers will work down
to 9v so no problem.

Jim

ps: avoid thermal trips if voltage loss is an issue.