I have not tried disconnecting the F850 for a longer period, so this information might not be relevant. But on all my previous BMW bikes, disconnecting the battery is no big deal, especially if it is for only 10 - 15 min. However, if the battery was disconnected for a longer time, there are 2 things that may matter.
1: The fueling of the bike is adaptive, and the bike adjust the fueling as you drive. If you change the exhaust system, the ECU will readjust, and store the adjusted values.
The type of memory for storing these adjustments needs a bit of power to be stored. If you remove power for more than 30 mins, the adjustment values will disappear.
But this is not a big deal. Once the bike is started up again, and it will start with no issues or no harm of any kind is done to the engine. As the engine runs, it will readjust again and slowly rebuild the correction map.
2: There is a built in clock that (in addition to the one shown in the TFT. And in addition to time it also stores the date. If power is removed, the date and time is zeroed out, and needs to be reset. This was not possible through the TFT. The internal clock needed to be reset by a diagnostic computer. As for running the bike with the wrong date and time causes absolutely NO PROBLEM to the rider. But the service reminder may get screwed up and the Service reminder may come on. But this is merely a nuisance. motoScan or GS911 will allow for this date and time reset. My mentioning about the potential not relevant might be that the TFT perhaps now resets the internal clock as well, so no Service reminder will be displayed after a long time disconnect.
The bottom line: If someone wants to disconnect the battery, go ahead. No problem, Nothing will be damaged or ruined. No essential software will be ruined.
The software that the dealer may have had in mind might be the adaptive map in the ECU, But this is a map that keeps correcting small values throughout the bikes lifetime. And zero out this map is temporarily, and may in worse case mean that the bike will not fully meet the emission values for a short while, until the map is rebuilt by the ECU.