Okay so I'm trying to bring the Sha'ir from 2E into 5E via homebrew. How I'm having it so far is that they player has a little helper called a Gen, a mini genie who gives them a bunch of neat benefits.

The key benefit is, depending on which elemental plane their Gen is from, they get a different series of spells as a part of their expanded spell list. Problem is, not matter what I do, the spells are being automatically added to the warlocks sheet and I KNOW that that is not how they are supposed to work. Going off of the Fiend, the expanded spell list doesn't add them to your list automatically. It just gives you more options to choose from when picking your spells. But, because I had to add these not in that little box under the main description of the subclass and instead in the area where you give a class extra spells, I can't seem to find a way to word these spells mechanically so they aren't added to the warlocks spell list and messing up their numbers for "known spells"

Please, for the love of all the patrons and beings of unfathomable power, how does one fix this problem?

Just make a different version of the subclass for each plane, like the circle of land druid had to do (for this same reason).

I can't, as the whole point was to be that they could switch back and forth between the different Gen. At this point, I might just have to get rid of the whole idea of switching back and forth and give them general elemental spells and say "screw it, you made a pact wit genie-kind as a whole figure it out why you'll later be able to control air and water."