The issue isn't damaged submodels, the SEXP can repair the submodel - but how do you justify an entire sheared off ventral engine section popping back into life when repairs are complete?
Easily. First, the Terrans activate an electron-matter ionizer by plugging into the damaged subsystem's Mjolnir socket. Several small charging tubes are assembled and placed near the broken or missing hull. The nanites are delivered via several gerbils that go through the tubes. The nanites then canabalize the gerbils, using their atoms as the building blocks for new matter. Using several low-level atomizers combined with a few high-level ion synchronizers, matter can be rearranged into different densities and new matter can be formed. Prior to the matter being finished, it usually remains in an invisible gaseous state until the point of completion, in which the newly made matter snaps suddenly into existance. This must be countered by using several magnetron emitters, and as such they are usually fired up prior to activation sequence. The whole device fits in a pen.