illegal sub?

[Gre144]

Jones reenters the game in the 3rd inning in the wrong batting order, therefore becoming an illegal sub under fed rules. In the 7th inning, he bats in the correct order and hits a homerun. The defensive coach finally realizes that Jones didn't bat in the correct order in the 3rd inning and calls for the enforcement of an illegal substitution right after Jones hits a homerun and before the next pitch.

1) Does Jones illegal status still exist thus nullifying the homerun, and causing an ejection and an out?

or

2) Does the homerun count because Jones is now batting in the proper order?

Greg