A further update...
The problem appears to be the flush valve for the watermaker. If it leaks from the freshwater side to the seawater side, when in the seawater position, it will send freshwater to the seawater distribution manifold. If you have the seachest thru-hull valve open to the sea, this won't be a problem. If you have that valve closed however, and the flush valve leaks as noted above, it will pressuize the seachest and force water back to the lowest reservior, which turns out to be the generator on an SM2000.
Don't close your seachest thru-hull while on the hard until you confirm no leak. You can do that by closing the seachest thru-hull, emptying the seachest, leaving the water pump on. If you don't get any leakage back into the seachest after 24 hours you're probably OK.
Thanks to Bob from Rossi Design Group (I didn't catch your boat name Bob) for the heads up to check this. I hope he will post any further information he has or correct any mistakes in my notes above.