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Confusion with Portugal's immigration, affecting new visa application?

I have lived in Portugal, and had a 1-year visa. I was not able to get an AIMA appointment during this date and was advised by AIMA that I didn't need one until it had expired. Immigration appointments are impossible there; calling hundreds or times and emailing every day does not help. I was told that all visas were extended, therefore, I thought mine was too. I have a full-time working contract with a Portuguese institute. Now returning to the UK I was told my visa was not part of this extension. Essentially, when my visa expired at the end of August, I have now overused the 90 days from then. I am appealing to VSF to make a new visa. If I provide all evidence on the cover letter, will this overstay without knowledge be accepted?