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I have a homebrew Space Marine chapter with its own fluff and history, but I need help deciding where knights will go.
General backstory, they were a 13th Founding chapter who, on their way to battle, got lost in the warp for a few millenia without a Codex: Astartes. When they came out, (Past the edge of Imperial space, out of touch withany potential allies), they had to re-write one from basically scratch and memory. They're arranged into 13 'Companies' (13 Because of their founding number), but each company works more as a separate branch from which resources are drawn. A battle might have a half a dozen squads working together, each from a different company. 11th company, for example, is recon and surveillance, so scouts, recon vehicles, and a model who uses Tigurius's rules (The Prescient, precogniscant psyker) are all 11th company, and will send a recon team off with a raiding party. 7th company has all the basic troops. 1st is Terminators. Etc.

However, I don't know where Knights would fit in. There are a couple options, but I can't decide which works best.
Option one: 13th Company. Kinda their Titan company. managing their super-heavy vehicles. (Their Thunderhawks and only actual titan, a single Warhound which they had with them when they were lost.)
Option two: 12th company. These guys are all management, support, and they hire mercenaries. They manage fortifications, tech-priest/servitor repair squads, and hire off useful warriors. (Mainly 'Rogue Trader' mercenary counts-as using Inquisitor rules and the like. I'd like to include Assassins, but that means bringing in Grey Knight rules which I don't want to do.) Since Knights aren't owned by Space Marines, it might be something they outsource.

I'd make the Knights a knightly household that operate with the chapter out of old oaths. rather then part of the space marines. titans and knights are not operated by marines in canon, but are rather basicly deployed as allies

Knights DON'T fit into the SM chain of command at ALL.

They are noble houses with ties to the Admech.
Separate again to the Titan legions.

A household with ties to the marine chapter (perhaps the marine chapter's recruting homeworld)?

I believe that there are Knight mercenaries, which is how they explain the silly allies matrix that allows Tau and Dark Eldar (but not Chaos, grr).

Also "they lost it" is almost comedic. Really you should just say that they decided to deviate from it without completely throwing it out, like a lot of Chapters.

Could be a freeblade who's allied with the chapter for whatever reason they feel like.

1) Knights has nothing to do with SM and heir chain of command.
2) Which doesnt stop you from fitting them into your fluff!
3) Lets just say your Knight was ordered to support your SM chapter in campaign and got lost in warp with them.
4) Or after re-emerging from warp, the old noble house on Knight World still exist and honors old allegiance to IoM and this specific chapter -> so some Noble rides his Knight to war by their side again.

The pilot could have died. Humans are frail. Given their dire situation, the superheavy walker in their cargo hold would be of great use to them.

They were also lost for "a few millennia". It's entirely possible that the pilot's Knight (are the pilots called Knights? If so, does that make it a Knight's Knight?) couldn't be returned to his/her House (as the Marines perhaps intended) because it no longer exists for some reason. The planet could have been sentenced to Exterminatus - just because you have Knights on a world and ties to the Mechanicus doesn't mean your planet is unable to be overwhelmed by heresy, Warp storms and daemons, Orks, Tyranids, whatever. Or the House simply faded, a victim of the constant passage of time.

Or, as n0t_u said, it could be a Freeblade who is with them for any reason.

I'm thinking of a Freeblade that vowed to serve my homebrew IF chapter. The chapter would assign chapter serfs to the Freeblade. Once the Freeblade aged out or was killed one of the better selfs would then pilot the knight.