I promised to update the forum upon my return back to Portugal, and so, here it goes:
My wife and I hold U.S. Passports and now live in Lisbon even though our residency cards have not yet been issued. We have completed, however, our biometric appointments in January 2023 and received documents that stated our completion of appointment (with no pending items to be provided). We left for the U.S. in February 2023 and returned back in Portugal in April 2023, staying out of Schengen for just over 60 days.
When we were boarding the flight with British Airways (LAX - HTR - LIS), they could careless about our stamps in our passports, just as long as our passports were valid. Now, when we missed our flight from London due to tight connection and were transferred on TAP, the agent did ask us to prove that we have a return flight from Lisbon. When we mentioned that we now live in Portugal, he asked to see supporting documentation at which state we showed him the SEF letter certifying the completion of biometrics. He was satisfied with that.
Upon return to Lisbon, the passport control SEF agent must have had information about our immigration status, but was unaware that we still had not received our cards. When he saw our passports, he stated that “… you must show your residency cards”. We were once again obliged to present our SEF document of biometric completion. He was satisfied, and slapped another stamp onto our passports.
The morale of the story: you might need to prove your SEF application status, but you will get your Schengen stamp re-set for another 90 days. Currently we are in Spain (though we drove here), and so far - so good.
Good luck everyone.