AIMA appointment postponed and Schengen visa expired.

I had an Article 15 appointment on the 2nd of April which was rescheduled by AIMA to 3rd July at the very last minute. My Schengen visa has now expired waiting for the appointment.

I need to travel back home else I risk losing my job so I plan to apply for a Schengen visa again and come back for my appointment.

We have tried to email and visit AIMA in person to get an earlier slot but not been heard.

I will be flying out of Lisbon so the question is:

1. Will I be treated as an overstay by Portuguese immigration and face problems acquiring a Schengen visa to come back for my appointment.

2. Will the new EES system capture this overstay anyways even if the Portuguese immigration doesn't treat it as such?