Yes. The report must be filed by the transferor/sender federal firearms licensee (FFL) regardless of whether a transferee/receiver FFL and/or the carrier indicate that they have filed a theft/loss report with ATF.
This requirement applies because only the transferor/sender specifically knows how and when the particular firearms were shipped. The transferee/receiver or the carrier most often does not have all of the information necessary to file a complete theft/loss report. The reporting requirement also applies because the disposition records of the transferor/sender FFL must be corrected to reflect the theft or loss.