That is a puzzlement for sure. But I've learned that many boat issues don't make sense.
I also have two A/C units, a 16 and a 5 like you. It sounds like we both have the same setup. I assume that the A/C systems are operating properly and that the main 16K unit shows a discharge and is not blocked. Given that is true, I can't think of any reason why you can't get AF to run through it. I suspect that the AF will flow from the 16K unit, but due to more flow resistance (for unknown reasons) it takes much longer than you expect.
The first year I winterized my systems, I found that a huge amount of AF was wasted out of one discharge while waiting for the other one to show AF. I solved this problem by adding two shutoff valves so that I could force the AF through one A/C unit at a time. This cut my AF usage by probably half. In your case it would also force the AF through each unit independent of the other. That should solve your issue.
For this year, you could simply disconnect the lines from the pump tee and drain as Jim has suggested above. To insure that you got all the water out from any unseen low spots, you could pressurize the lines with a compressor or a dinghy air pump, or you could attach the lines to a wet shop vac and suck out the water. Your choice, whichever is easier for you. For an easier time next year, read on....
In this picture below you can see the two 1/4 turn valves I added. The tee and check valve noted at the bottom are for a take-off to the anchor washdown pump and to the galley seawater faucet, and have nothing to do with the A/C valve arrangement.