It took me a week and a half to figure this out, so I thought I'd make a post here to share with everyone. While some buildings are destroyed outright by a single point of damage, some are not. Should a large building (tracking station, commercial freight facility, ground force training facility, shipyard, naval academy, spaceport, sector command) be damaged by bombardment, it can be 'repaired' by building a fraction of a building.
For example, if your GFTF takes three hits during planetary bombardment, it will be reduced to 0.85 of a GFTF, and can be repaired by ordering your construction factories to build 0.15 of a GFTF. Conveniently, you can bump this repair order up to the top of the queue. Sadly, any unit it may have been training at the time is toast.
