QAfood,
I don't really understand your question. If you scheduled an actual SQF audit with an approved Certification Body I can't understand how they could change that to a pre-assessment audit. Pre-assessment audits are optional. Are you sure that whoever scheduled the SQF certification audit (document and facility) didn't also schedule a pre-assessment audit? If this is the case it's actually a good thing from a "results point of view", but will set your timeline back a bit.
A pre-assessment audit is essentially a "warm up excercise" for an actual audit. It's generally recommended to have this done by the CB you're using (and specifically the actual auditor scheduled by the CB) to perform the actual certification audit for your facility. In my opinion this gives you your best chance of acheiving good results (auditor consistancy = good).
During the pre-assessment audit the auditor can tell you where your company has non-conformances or gaps in your SQF system but if this is done by your chosen CB for the actual doc & facility audit the auditor can't consult (i.e. spell out exactly what your corrective actions would need to be to become compliant in each non-conformace noted). Best practices can be shared (nudge and a wink).
In my case the pre-assessment audit took place about a month prior to the document audit. The facility audit was done about 2 weeks after the doc audit was finalized.
A bit confusing, I know, but that's the simplest I can put it. Good luck!
Regards,
esquef