Hi I’m the Firmware Developer of the CB3. There is currently a issue where the Bootloader sometimes overwrites the UserConfig while doing a Firmware update (chances this happens are about 1/5, depending in where in NVMEM the config is currently written to). This will be fixed in the upcoming Firmware (0x26510900). You can just load a backup and it should be fixed for now.
The upgrade to the next Version (26510900) should be the last time the config can be lost.
deCONZ and HA should automatically create periodic Backups that you can apply if your config gets lost.
But like @dduransseau said its good practice to always do a backup before the firmware update and apply a backup after.
Best Regards
Eric