They have confused two processes here. Under NEC3, there are only three deemed acceptances in the whole contract and they are all to do with compensation events. If an early warning has been notified, it is added to the Risk register by the Project Manager and either discussed at a bespoke risk reduction meeting or the next risk reduction meeting if one has been scheduled. Early warnings are for things that might or could be an issue and the idea is you discuss it to minimise or avoid its potential impact.
If this matter IS now a problem and a reason under 60.1 for being one, they should notify (separately) that this matter is a compensation event. That requires a response within a week from the PM. If there is no response, the Contractor can notify that there has been no response, and it there is not further response after another two weeks it is deemed accepted. There is a similar deemed acceptance loop is there is no response to a quotation, or if the PM said they would assess themselves but then did not.
If this matter IS now a problem and a reason under 60.1 for being one, they should notify (separately) that this matter is a compensation event. That requires a response within a week from the PM. If there is no response, the Contractor can notify that there has been no response, and it there is not further response after another two weeks it is deemed accepted. There is a similar deemed acceptance loop is there is no response to a quotation, or if the PM said they would assess themselves but then did not.