Hello, first post from a long time lurker. We just passed an SQF Level 2, and this is one of the topics we struggled with as well. For background purposes, we are a 3rd party toller of dehydrated vegatables with milling, blending, sorting and packaging operations.
Our cleaning programs consist of:
-post-production cleanups of the production lines and surrounding areas (various mill types are their own lines, the cone blender is its own line, etc)
-pre-op checklists to verify cleanliness prior to start (and instructions to reclean if an item is dirty, such as the floors)
-master sanitation schedules (we have a custodian full time on day shift, the sanitation schedule for his duties covers some of the "easy to miss" areas such as corners, warehouse perimeter, overall floor cleanliness with a floor scrubber, etc)
To answer your question on "what will an auditor do", the answer is you'll get a non-conformity. Period. We took a couple minors related to cleanliness. Our facility is like you describe: a warehouse with many areas for dust to accumulate. One hit was due to an auditor finding dust/debris inside an equipment motor housing. We missed that particular area because it's on a production line that is non-operational (and hence, we don't have anyone actively cleaning it post-production). We addressed that in the audit response by adding a check and clean of idle production lines to the sanitation schedule on a bi-weekly basis, meaning even if we aren't using a production line for an extended period, someone will check for debris and clean it if debris is found.
The other hit we took was product debris on an metal detector. Now, the metal detector had just been returned from maintenance, where it had been for a week following a failed operational test. When we pulled it from service, it had been in production, and it uses a food grade belt to transport product through the detector prior to packaging, so obviously product debris was on it when we pulled it. That morning the detector had been returned to an idle packaging line, maybe an hour before the auditor found it, so we hadn't had a chance to clean it prior to the auditor finding it. Our mistake, we've rectified that as well.
Those are my experiences thus far with the SQF audits. This December was our first one, and we were very happy to pass with the "good" grade. These guys are very through. If you've got a dirty part of the warehouse, he's going to ask when it was last cleaned. He's going to ask who's responsible for cleaning it. And he's going to ask for the DOCUMENT that shows you clean that part of the warehouse, with the frequency schedule. Hope that helps answer some questions.