Deep ATG squats and long-stride lunges are what an unhappy ankle tends to object to. Impact work — jumping, sprinting — too, though RepRoute doesn't program your conditioning.
The ankle tag is the one tag in the catalogue applied selectively rather than across a whole pattern: roughly half the squat variants and about half the lunge variants carry it, and nothing else does. So flagging an ankle removes those specific movements and leaves your presses, pulls, hinges and core work completely untouched — and usually leaves you some squatting too.
As with every flag, the engine removes; it does not lighten or shorten. Any day left short is refilled with up to three exercises from the patterns still open to you.