Per the instructions on ATF Form 3310.11, "Should any of the firearms be located, they should be re-entered into the Record of Acquisition and Disposition as an acquisition entry, and notification should be made to the Stolen Firearms Program."
The original disposition with the theft loss report should stay intact as the gun was out of your control for a period of time.
The firearm must be logged in from the entity that returned it to you, whether that is the local PD, another entity, or your FFL.
You must contact the Stolen Firearms Program (and the local police to whom your reported theft if needed) to report the recovered firearm at 888-930-9275 or via email at firstname.lastname@example.org.
In FastBound, you will create a new Acquisition and enter or select the contact that returned the Item. e.g. Police department, shipping company, or your FFL. The acquire date will be the date the Item was returned or found.
It is recommended that you make a note on the Item saying that it was previously reported as theft/loss and recovered.