Canon that does not respect it's own canon is not canon. It is retcon.
I know exactly what retconning is, it is when canon is changed retroactively to fit something new, there is not a single explanation for the "new" armour design that does not bend canon over a fence. Therefore it is a retcon.
They could have explained it better if they put more work into it, made Cortana say "I used some classified schematics to redesign your armour", or started the game off in the classic MKVI and given you the upgraded suit once you reach the Infinity.
But no, the implementation screams retcon, and it works as a retcon, they overhauled the aesthetic and design of everything else in the game, it's just a retcon, but nooooo everything else is artistic license, and the armour is the only change that's canon.
Halo 2 starts off with the Gunnery Sarge telling you about your new suit, Half Life 2 has Kleiner state that he made modifications to the HEV suit, when things change, address them in game, don't come up with a half assed explanation that doesn't hold up under scrutiny.
If you won't accept H2A, then explain the fact that the original Mark VI is present canonically among the Spartan IVs (both in the multiplayers of Halo 4 and Halo 5, not to mention it's appearance in H2A's multiplayer, which wasn't trying to be accurate).
This is the problem with Infinity Slayer being brought into the canon, this is like trying to explain why the MKV helmet is in Halo 3, or the MKVI helmet is in Halo Reach. It's in there for fan service and extra variety, it is not canon.
As for why she didn't repair the damage, the best explanation I can offer is that it was due to her rampancy. I mean, she attempted to kill Chief at least once near the end of their journey thanks to her rampancy, not fully repairing his armor isn't the worst she's done.
And just like any other explanation for the armour, that doesn't hold up under any scrutiny.
If you absolutely insist that it must be a retcon despite the original Mark VI still existing in canon, then why can't it just be a "retcon" that gives Mark VI nanotech?
What is the difference between admitting that the MKVI redesign is a retcon, and that they added nanotechnology to the MKVI to facilitate the redesign?
There is none, retcon occurs either way, retconning the appearance just makes more sense.
The entire series has a new aesthetic, there are too many inconsistencies and problems with trying to explain the redesign in canon. It's a retcon, just the same as every other aesthetic change in the game. They changed the armour to fit the new aesthetic, and changed their mind about it when it was too late.
It is a retcon. Fact.