I think it is extremely unlikely that a C&R holder will be audited. Some red flags, FWIW. Buying large quantities of guns, especially handguns, under your C&R. Buying a couple of guns to pick the best is OK, but buying 5000 guns to arm the local mafia or your friendly militia is going to raise alarms.
Another red flag is having a gun you bought under your license turn up at a crime scene or in the hands of some guy on parole for serial bank robbery.
If you play by the rules (and don't try to push the envelope to see what you can get away with), you should have nothing to worry about.
Note that since a C&R holder is assumed to carry on his collecting activity from his house, not a public place of business, any search will require a warrant. They can inspect your book, but you can also say that you will bring them the book at their office.