The reason we advise doing an initial assessment for patients who are being referred into the practice is that if they do not show up you will have the initial triage form filled in already so you can then TC that and put a check in failed to attend for their face to face appointment. If you do not collect this data then the patient fails the appointment you will not have anything to send. I have confirmed with the BSA that if you do a phone triage and make an appointment that the patient FTA's you would still be expected to send off the initial triage.
If the patient does attend their appointment you can leave the initial assessment there the full FP17 will still be generated and there will not be an issue with the claim or if you would like you can move it onto a private COT and send it to history (tick it as complete then right-click and choose send completed to history) then send off the banded treatment and the in treatment triage on the NHS COT.
In regards to your patients coming in for routine exams/treatment, the initial assessment does not need to be filled in but you should add the in treatment triage which populates that patients COVID-19 status on the FP17/O.