Updating the bootloader seems possible through a different firmware file, see: page 79 of this thread. Please go from there
Also, here is some info on unique capabilities of the older boot version: How to downgrade DS1000Z FW
How well your scope likes the new firmware without boot version update, I don’t know. In case you are fearless and go for the whole experience, please let us know how it all went and also:
If someone can point us / me towards the latest "Boot Version" update file, that would be nice. I would want to include that in the buglist / update thread.
Post #1964, on page 79 of this thread, mentions version 04.00.00.00 as the last one confirmed to include a boot loader update. A copy is hosted at
http://www.gotroot.ca/rigol/DS1000Z-04_00_00_00.7z (in 7-zip format, whatever that is...). There is contradictory information on that page whether the later 04.01.02.00 also included a boot loader update.
Also some unclear statements in posts #1968 ff. whether that old
boot loader update can still be installed once you have a more recent
firmware in place. The posts seem to say that the answer is "no", but I am not sure whether everybody clearly distinguished between boot loader and firmware there. (We know that it is not possible to downgrade the firmware. But does Rigol really prevent you from upgrading the boot loader, if the firmware version has been upgraded even further in the meantime? Doesn't make sense to me...)