I have mistakenly ended up with my little-used SkyMiles number on a DL ticket instead of my WP number. The miles went to my DL account. It's the only time I have had to get the WP Service Center involved, but they did fix it for me. The only way I can think that this happened is that I had "Remember Me" checked on the DL website. When I pulled in my reservation by Conf #, the WP FF# magically got changed to the DL SkyMiles #. If you ever look at your DL itinerary on the DL website, make sure you are not signed in and make sure you pull up the reservation by Credit Card # or Confirmation #. In other words, just pretend you never had a SkyMiles #.
Someone also said that if you buy a gate upgrade on DL metal, they make you enter your SkyMiles number. This is not true in my experience. I flew on DL last year. I was so exhausted from SkyWest's butchering of my inbound flight into SLC that I bought the upgrade at the gate on the connecting mainline DL flight. I had my Continental OnePass number in the reservation, and there was no problem. The miles showed up in my OP account. I would expect the same would have happened if I had had my WP number in the DL reservation instead.