The following assumes you are normally fully resident in Portugal, as opposed to resident in the UK with extended visits to PT as and when.
It has never been a legal requirement that you obtain the permanent residence certificate (eg it's not a document that you can be fined or otherwise sanctioned for not holding, unlike the initial residence registration certificate), so there shouldn't be any notion of there being a set period for applying for it around the time of expiry of the first certificate.
There's also clear mention in Brexit-related material released by the PT authorities that currently unregistered UK citizens living in Portugal merely need register before the end of the transition period to formalise their status, and acknowledgement that some will be entitled to apply for the permanent residence document straight away. This means there can't be any Go Back to Start if you've a lapsed 5 year initial registration certificate, although presumably you'll need to substantiate in some way that you have actually been continuously resident in Portugal, as defined in the relevant legislation, during the previous 5 years.
I'll give you an example of the above from an authoritative source :
I HAVE THE RIGHT OF PERMANENT RESIDENCE IN PORTUGAL, BUT HAD NEVER APPLIED FOR THE RESIDENCE CERTIFICATE ATTESTING THAT RIGHT. SHALL I APPLY FOR IT BEFORE THE END OF THE TRANSITIONAL PERIOD?
The right of permanent residence for UK nationals residing in Portugal under the Withdrawal Agreement is not dependent on the residence document (although, in Portugal, registration is mandatory). However, it is advisable that, before the transition period ends, register your residence within the City Council of your area of residence (for residences under five years old) r within the Immigration and Borders Service (for residences with more than five years).
BREXIT - FREQUENTLY ASKED QUESTIONS
I imagine you'll be anxious to get over to Portugal at some stage before the end of the transition period to get this sorted if you can but hope that helps to set your mind at rest in the meantime.