At least I know the behavior of first burning a bootloader via the IDE and then uploading a sketch with the IDE upload using programmer, results in the sketch being installed but the bootloader being erased.
Or, the fuses are set to Not point at the bootload area as the starting location, but instead at the sketch starting location.
Section 27.2 of the datasheet:
The program code within the Boot Loader section has the capability to write into the entire Flash, including the Boot Loader memory. The Boot Loader can thus even modify itself, and it can also erase itself from the code if the feature is not needed anymore. The size of the Boot Loader memory is configurable with fuses and the Boot Loader has two separate sets of Boot Lock bits which can be set independently.