For a company I worked at I was the full time Practitioner for our one site, but would consult and assist for two of our other sites. First thing, each site needs a designated SQF Practitioner and back-up. You as consultant can be neither. Possibly could be the back-up, but you'd have to be on site when the main Practitioner is away during audit time.
I was allowed to assist during the audit, but each auditor made it very clear that the site's Practitioner should be the main person leading the audit. During one audit I consulted with, the sites Practitioner kept looking to me to answer...that lasted maybe an hour before the auditor stepped in and said 'I am convinced he knows, but you are the main Practitioner for this site and need to know and answer these questions as well'. So you can assist, but the site Practitioner has to know and show they understand the program.
Finally, during an unannounced audit, the auditor will not wait for a Practitioner to show up to start the audit. This is why you are to have a Practitioner and a back up on site. They have to start the facility inspection part of the audit within the first 30 minutes of arrival. So if they arrive and the main Practitioner is not there, it falls on the back-up to run the audit. So either the main Practitioner or the back-up should be on site during your normal business hours during the unannounced audit period.