The HLOS plans did include alternative options in some cases, opposed to having one option set in stone.
A couple of months back someone was commenting that XC should have got a couple of extra 170s off LM under it, when it turned out the plan for increasing capacity in the East Midlands included two alternatives - one for the 170s off LM which was not implemented and another for EMT to get extra 153s, which was implemented.
It seems the option to send 317s to c2c was still there but the alternative option to send 321s to LM was not.
With NXEA happily keeping the extra units in service when the 379s were introduced and c2c not pushing for extra units it got forgotten about until Abeillo stated that 9 of the units aren't required to meet the franchise commitment.
I've found the original DfT statement, from Jan 2008, which reads:
"1. The additional vehicles on C2C [40] would be cascaded EMUs likely to be
either ten class 321 units from London Midland
or ten class 317 units from the One franchise.
2. The One franchise would take on lease class 321 units cascaded from London Midland. In addition, the franchise would order new EMU vehicles for services on the West Anglia route to Stansted airport, in turn releasing Class 317 vehicles to provide more coaches on other services [IMHO that means other services of their own]."
The 'One' franchise's net increase allocated in the associated table was 188 vehicles which turned out (as we now know) to be 120 x 379 and 68 x 321. It seems to me that if ten class 317 had moved from One to c2c then 'One' would have had to get 10 more 321s from LM as well to balance the books and keep that net increase of 188 vehicles.
So as far as the HLOS went, 'One' were due 188 vehicles, and that's exactly what they got; therefore I don't think the 317s are 'spare' specifically because they didn't transfer to c2c, because if they had gone there NXEA would have still ended their franchise with the same number of extra units by other means. What has made them spare is more likely to have been the new franchisee not having to provide 12 car Stansted Express trains as originally planned.