FFLs must report the Theft/Loss of firearms to the ATF Stolen Firearms Program Manager within 48 hours of discovery (toll-free) 888-930-9275. This call must be followed up with the filing of a paper report, ATF Form 3310.11.
This 48 hour period does not start until you've exhausted all efforts to locate the item(s) in question. However, this means actively searching and the period is not indefinite. If ATF inspects while you are "searching," they will cite a violation.
Reporting a missing firearm is not a violation, but failure to report one is.
For more information consult the FFLGuard Help Desk