Starting from HQ level 4, you will see an additional button at your home base:
Tapping this button will open a pop-up screen that asks you to confirm the reinforcement of your Landing Crafts with the same troops held previously.
The same button also appears on the Archipelago map after an attack:
So if you lose some Comrades during a raid, you can refill Landing Crafts with the same troops by tapping that button.