the prefix code should have had a reference later in the movie as well... imo
after the enterprise counter attack the reliant withdraws. off screen she goes to regula and tries to get genesis. kahn cant find it then goes back to reliant. jocamin then says impulse power restored after kahn gets genesis. we then see the reliant approach the station expecting to find enterprise.
so my question is, why the need to restore impulse power before attacking enterprise? photon control and warp drive were what the counter attack knocked out. but a shielded reliant should have still been able to best the crippled enterprise. now if jocamin came up and said something to the effect of the codes been changed or weve regained sole and full control of the reliant then it would make sense that they hadnt gone and attacked the enterprise.
but maybe im over thinking.
It's possible that as Reliant
was retreating, additional damage may have occurred due to fires, power surges, etc.
Remember, Khan was trying to run a ship usually crewed by at least 300 with a crew of about 60. Even Enterprise
with a full (admittedly mostly cadets/trainees) crew faced huge damage-control issues.
Khan wanted all the chips stacked in his favour, so waited until all the systems were repaired. After all, he knew the Enterprise
wasn't going anywhere, and he had no intention of making the same mistake as he did in their first encounter.