The preps can be done elsewhere, just take out of rotation, for example getting the drills or whatever for the different heist, there's other construction zones that already have the same preps happening in them and those can stay while you removed the skyscraper one.

Hardcodded missions (i.e. that don't take part in the regular freemode session) are trickier but those can either be removed (Rockstar has already removed a variety of jobs, for example Overtime Rumble) or do some trickery to load in the assets from elsewhere (either a different instance or instancing directly from Story mode), the later takes time and work but is not impossible specially if they decide to make something big with the building while just removing outright is easier (and again, not unheard of from Rockstar)