I haven't seen the MCU's, but this is an educated guess. The MCU has what is essentially a hard drive storage on it. It's not a spinning disk, but is an SSD technology. I expect that the early versions of the MCU had this storage soldered onto the MCU motherboard and removing it would run the risk of damage.
I would not be surprised if they changed this to a removable storage. Possibly even going with a commercially available SSD mounted on the MCU board. The processor for MCU 1 was an Nvidia processor and all the processors post MCU 1 are Intel and probably similar to one another if not the same. Popping a removable SSD off the old MCU and placing it on the new one would be easy to do in that case.
But changing processors, even if the SSD could be easily moved would require a fair bit of work replacing the drivers for the different processor and there may be other code issues that would take someone with a fair bit of computing skills to fix. So it's simpler just to tell people upgrading from MCU 1 that they will lose all their information and settings, but other upgrades can be done without losing data.
I don't know for sure, but this is my guess from being an Electronic Engineer and having built PCs since 1987. I'm just making some guesses about how the black box works.