At this point, I would just start grinding out missions working as an employee to earn enough to start fixing things. After an item is fixed, maybe take the company plane up in an easy mission to see if it got your flaps working again. Tedious yes, but it should eventually get the flaps working again. But I’m also just stubborn like that.
See if any of your fuses are pulled on the fuse panel, especially any related to flap operation.