Apologies to bump an old thread, just wanted to drop a datapoint in case anyone else runs into this issue of PNRs being "held" at checkout.

I booked an ANA award with LifeMiles and ran into this exact issue (2 seats freed up, started checkout process with one pax instead of two, when I went back to re-do it one ticket was "gone"). I had noticed at the time that lifemiles already gave me a PNR even before completing checkout/payment (which funnily enough works on ana.com). Hoping that the first seat would become available again, but wanting to secure my chances, I booked the first pax as a single booking and waited for the second seat to become available again.

The "temporary" ANA PNR created during checkout expired and released the seat almost exactly 1 hour after getting to the final checkout page. So if you've accidentally "locked" an ANA award, I would suggest waiting one hour. Alternatively try calling LifeMiles but I didn't manage to do this in time. Anyway, 25 USD poorer now that I had booked two separate awards, but lesson learned.

Don't know if this applies to other bookings etc. Through some experimentation I could confirm that this checkout process completely removes the seat from availability (other award sites can't find it either while it's "locked").