The Wild Shape feat gives you the Wild Shape order spell, which lets you turn into various forms that are found in polymorph spells. Precisely, Wild Shape grants you the forms in Pest Form on 1st level, the forms in Animal Form on 2nd level, and then other feats do this:
Add the forms in insect form to your wild shape list.
Add the bat and bird forms in aerial form to your wild shape list. If you have Insect Shape, you also add the wasp form to your wild shape list. If you have Ferocious Shape, you also add the pterosaur form to your wild shape list.
And so forth.
Now, the Form Control feat has this effect that lets you prolong the duration of Wild Shape at the cost of lowering its level:
If your next action is to cast wild shape, wild shape’s spell level is 2 lower than normal (minimum 1st level), but you can remain transformed for up to 1 hour or the listed duration (whichever is longer).
Now, to the question:
Do you lose an option from the Wild Shape list if you use form control and the level of wild shape is lower than the level of the original spell?
First things first: Since Animal Form is explicitly granted as a heightened option on 2nd level, if the level of Wild Shape should fall below 2nd with Form Control, the Animal Form options are no longer available.
But what about the Insect Form options? These are gained via the Insect Shape feat, not via Wild Shape’s level. I first assumed that if Wild Shape is on level 2 with Form Control, the forms of Insect Form (which is a 3rd level spell) are not available. But the text doesn’t mention casting Insect Form. It says "Add the forms in insect form to your wild shape list," and Wild Shape says little about its level. I think there are ancestry feats that grant you higher-level spells on level 1, that could serve as a precedence here, but I can’t find them at this time.
But if you keep the forms on your list, what’s the drawback of lowering the spell’s level? You lose Animal Form until you’re level 7, and you are easier to dispel?