I have a dual nationality and due to thieves one of my passports had to be replaced last year.
My Portuguese passport is still valid but because it had been connected to my old british passport through my european union citizenship I would now also like this replaced
Firstly can you advise me if I can make an online application and secondly I would like a fee waiver as I paid for the renewed british one in 2016,I can provide a crime ref number regarding this

No you can't do it online. They have no idea WHO is actually doing it. You HAVE to go to your embassy or consulate in the country you reside, and PROVE your identity.