Hello ViaCirca,
uploading the original Behringer Firmware over SysEx works exactly like uploading the Zaquencer (press Store+Learn/Load at startup to put it into bootloader mode, then send firmware over SysEx). Note that once you´ve uploaded the original firmware, you either have to create a new controller mapping or upload an existing controller preset via SysEx (see BCR manual for that). This is because the flash presets get overwritten in both directions.
Another note: if you´ve written something in the Presets of the Behringer firmware and want to go back to the Zaquencer a Zaquencer flash reinit is recommended. In some circumstances the Zaquencer will detect it and trigger the flash reinit automatically. If not, you should do it manually by holding PAGE < (the left Page button) and STOP/PLAY during turning on the BCR. If the init is omitted, you could get garbled pattern info in the flash, possibly leading to all sorts of weird behaviour.
The original Firmware can be found at http://www.behringerdownload.de/B-Control_download/bcr2000_1-10.zip