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.
Mercenaries and borrowed troops
Mercenaries from events, and troops an ally lends you, stay only for their contract. When it ends they leave. Your free Reserves cover the departure first, so if your own troops of that type still cover what your squads hold, every squad stays full. Otherwise the squads give up the difference: other squads before your defender, back row before front.
A squad at home gives them up right away. A squad out on a mission keeps its troops while it is away and gives up what is still owed when it comes home, and a squad inside the Sunken Arcology keeps them until the run ends. A slot that is in your selected preset keeps its target and shows the gap, so the top-up refills it later; any other slot simply loses those troops. Your presets never change.
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.