PROGRESSION
Squads and the Barracks
Your troops live in two places: Reserves, the pool everything returns to, and a live squad attached to each ready commander.
Recipes, not snapshots
A preset is a recipe: a list of what you want in each slot. It owns nothing, and it is only written when you edit it yourself.
Your live squad is then kept at the smaller of the recipe and what is actually available. Whenever troops come back to you, from a mission, a hospital discharge or a finished training order, the server tops your squads back up toward their recipes from genuinely free Reserves.
That is why your squad refills itself after a bad fight without you touching anything, and why loading a preset while you are short is not an error. It fills what it can and tells you what it could not.
The wounded
Casualties go to the hospital and heal back into Reserves, not into the slot they died in. The top-up then puts them back to work. Nothing is tied to a commander while it is wounded.
Training
Training is a timer, and like every timer it can be shortened with catalysts.