I would still ensure that you do your best to ensure all modules are shut down to the best of your abilities as it will probably struggle to maintain the voltage/current required if the car has just been opened/awakened. A second battery or even car is also another easy option to do so with some jump leads.To avoid the problems that can come with disconnecting the battery on an FL, i.e. locking and other problems then buying one of these may stop the problems by keeping the modules powered
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Is there a connection point under the bonnet somewhere you can clip onto, as imagine it will be nigh on impossible to connect onto the battery clamps in the boot at the same time as disconnecting the existing battery, not to mention the danger of shorting the positive onto the bodywork by accident.
All well and good still but most people need to disconnect the battery for reasons other than simply to change it. Usually to change a module or remove a seat (airbags etc) in which case you need the system powered down regardless.