The system does not prompt for Cert collection on 1K Shuttle Upgrades. Sometimes a CSR will ask even before pulling the PNR if you say something about an upgrade or First Class (e.g. "how will you pay for the upgrade...") otherwise they smile and wave you on.

I actually flew from SFO to LAS to DEN (all Shuttle) and then DEN-IAH on mainline. And both SFO-LAS and LAS-DEN were happily upgraded to F without certs. DEN-IAH checked in full, so I had a nice bulkhead on the Airbus (which has more room anyway!)