I did make a new save for this, I have checked all of my missions, and they are all completed. Its so stupid that it doesn’t tell you whether you have completed the game with skulls on. It shows the difficulty, but not skulls. It is quite literally my last achievement I need to get 100%.
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Mines bugging on sequence and house of reckoning. Started it off a completed legendary campaign.
If I start again on a new save game, do I need to collect all the spartan cores to make it playable or can you get through without?
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I’m getting the same issue. Right now The Sequence and House of Reckoning aren’t tracking as completed on LASO on the Tac-Map. I already finished LASO in May, didn’t get the achievement then either. After the winter update I made a new save and ran through it on Easy to get all the upgrades easier and have been using mission replay to beat them on LASO, that way I can have all the upgrades to make it easier on me this time around and can tell that I did it on LASO after the fact. I’m waiting to replay these and beat the Silent Auditorium until this gets fixed/a workaround is found. It’s so frustrating.
Pretty much the same experience here, I sped-ran a fresh save on Easy to 100% completion shortly after the Winter Update dropped, to nab those new MP stances. Then I ran each mission on my 100% save on LASO using Mission Replay. Three of the missions (Spire, The Sequence and House of Reckoning) did not track and neither did the Headmaster achievement, sadly.
Thought I had to make an entirely new save on LASO for it to track but some folks here have tried that and still haven’t gotten their achievement yet. So I’m thinking we’ll have to wait until they address the issue in the new year sometime.
Hopefully (and ideally) they can auto-unlock the cheevo as compensation but that might be a reach. 
I just don’t fancy doing LASO again.
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I ALSO tried the easy run through for the upgrades post update. I have some notes to hopefully help some others.
I noticed with Outpost Tremonius, The Spire, The Conservatory, these missions stayed “easy locked” when I ran through them on LASO.
However.
I went back and replayed them on mission replay on LASO in Co Op and it changed to legendary. With one exception, The Sequence.
The Sequence will not change no matter what I do. I tried going solo, two man and a 4 man team. I tried clearing all the HVTs and FOBs prior to not confuse the mission and this still failed. So I am currently running ANOTHER easy play through but when I reach the spire, I will start running LASO co op see if it makes a difference to run LASO the first way through sequence and determine if it’s only mission replay that’s busted or the whole mission itself. I will keep you guys posted.
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The best way I got headmaster achievement on halo infinite is to find all the skulls wile beating it on legendary again then turn around on a new save turn all skulls on legendary beat it again hope that helps worked for me did it solo 
Yesterday, I did a single playtrough from 0 in LASO, a new save and all skull activated, no Tank gun, no skip or any funny Glitch. At the beginning it was hard but after I got the Sword, The Arcane centinel beam and thruster, it was a lot of fun and pain in the same way. After 9-10 hours, I got the achievement, that to say, this was my 5th try and the fastest one.
I had nightmares thanks to the Hunters, but here’s a tip: Sword and frag-granades, jump, dash and throw as many granades as you can. Use the centinel beam too, however it is a pain, the Hunter are always looking at you in close rooms, so it hard to catch them in the back.
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I just completed the main campaign in legendary, all skulls in under 8h unlocking the “Forza Veloce” achievement, but guess what, no Headmaster… Is this issue even solved?
Did you play through the campaign on a new save slot? And have you checked, if there is the symbol for legendary completion for each mission? Have you tried to do a hard reset for the xbox?