First of all, please don’t have pencils around. It can be erased, and that is a Good Documentation Practice violation. Everything should be written in pen.
Also, I’m surprised about the discussion of pens and particle generation. Paper generates way more particles than a pen ever could. Equipment generates more than paper ever could, and people generate (by far) the most. So from a risked based approach pens are a infinitesimally small potential source of contamination - unless you are using a pen I’m not aware of.
I think the response to the auditor, might be:
"We have a particle mitigation strategy which includes HEPA filtered air, gowning practices and procedures and hand wash practices, and followed up by a regimen of particle monitoring, and refer the auditor to your various procedures/SOPs.