Until what point can you no longer call...?

[referee99]

... a free throw violation?

Team A has 3 teammates (A2, A3, & A4) of the thrower lined up in marked lane spaces.
Officials don't recognize. A1 is shooting two free-throws.

Ball is at disposal of thrower.
Thrower shoots free-throw. Ball goes in.
Official takes ball out of the basket.

Say substitutes are coming in. Officials notice A4 leaving the top lane space (maybe even gets substituted for). Official begins puzzling. Team A is now legal, no 3rd teammate in a marked lane space.
Lead announces: "One" and bounces ball to thrower.

Ball is at disposal of thrower.
Ball is thrown by the thrower.
Ball goes in.
Team B takes ball for endline throw-in.
Team B's legal throw in ends.

My question is this: at what point (exactly) can you no longer call the free-throw violation on Team A? Say our puzzling official finally figures out that a violation on Team A DID occur on the first free-throw (which was made). When does the ability to call and enforce the violation end?