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Dan.  I am a UK national and, at time of application, early 2019 , it was pretty straightforward.
I am now resident NHR.
I did it on my own, no professional help.
There is a very good book, up to date and almost all correct by Blevin Franks.
I met with Adrian at Loule, near Albufeira.
They might be able to assist further if ask for a free consultation.
The book, moving to Portugal or something, can be bought straight from them at their website.
It costs less than 10 Euro and a great investment.

It's weird to be refused so many times.
Are there "valid" justifications for that?

/forum/viewtopic.php?id=911492

I am not sure.  The accountant I hired to perform the work has encountered many problems with process.  I am not sure if he did not comply with the government regulations to obtain the certificate.  I have my NIF number and a EU residency certificate.  My wife has a different name and she has an NIF number etc.   Her address was different initially for some reason but we corrected the address.   I was contacted by an accountant through EX-PAT and I will see if he can help.  I appreciate your assistance and advice.  Good luck and wishes for good health during these difficut times.

Dan

Can you give me Adrian phone number?

Well, have you tried a professional accounting firm in Lisbon. I was assisted by BDO, who have an office in Lisbon. They were very helpful and made sure that I get the NHR certificate almost immediately. Your conditions might be different, though.