Chances are the animals will be re-homed, first with fosters, and eventually permanently once the courts get done fiddling around. There is little likelihood that any of the animals will have papers at that point.
A number of years ago there was a well-known breeder in Wisconsin that had all animals confiscated. All were eventually placed in new permanent homes. All had been registered but the previous owner refused to give the new owners any papers and the court did not order her to do so. None had been previously DNA'd so there was no way to prove that those animals were in fact the one on the papers. The AMHA horses had pictures (this was before AMHR started doing pictures) but that was not enough evidence...and AMHA would not get involved in trying to get papers on these horses. There were some NICE mares in the herd, though most were in their middle to upper teens. A couple of the younger ones went to homes where they were hardshipped into AMHA .... again....but most ended up as pets.