These are just a few of the things we did when the FDA came to our facility ( but we make cheese =] ).
- Print a map of the facility for yourself and the inspector. Go with them when they swab. Mark down on your map the corresponding sample number and write down the specific area in a notebook.
- Take a camera and photograph each swab site.
- Clean and sanitize Zone 1's right after they swab (broth from the swab gets on surface, etc).
- Write down the lot/batch and type or product that will be run that day. Hold until results are back, if possible.
This is good advice. What's also helpful is that they gave you a heads up that they would be swabbing. I don't think there is value in duplicating their swabs -- it increases the likelihood of presumptive positives, errors, etc. and if they get a positive and you get a negative, your negative will mean nothing to them.
If your production schedule normally has a clean at the end of each day, I would be hyper-focused on ensuring SSOPs are followed exactly and that you carefully inspect for niche areas. Have a plan to bracket and keep on HOLD the production that would be affected by the swabbing activities until you get results back as CRLamb mentioned. Even if you test finished product for Salmonella, if you get hits on Z1 surfaces you wont be able to convince them that you don't have conditions whereby product may become adulterated. They can also hit you with the 'conditions wherby' with having a lot of environmental positives in Z2-3 if they see enough GMP issues.
Once they've finished swabbing and inspection activities, if scheduling permits, to ensure a clean break, I would clean and sanitize the line and conduct environmental swabbing that would cover the same sites.
Best of luck.