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The Di2 USB charger includes PC interface gubbins.
AFAIK you can't use the external battery mount with the newer versions of Junction A that include a charging/PC port - it'll simply refuse to function. Therefore you need the old Junction A that doesn't have a charging port (used to be <£10 on ebay).
If you still need to update firmware with this setup you need to buy/borrow the PCe1 e-tube interface (£££ and pretty rare, though a good LBS might have one).
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@user136820
I bought an external battery mount to make a custom Di2 battery pack but the mount doesn't work with the rest of the components when supplied with 8.4V. So I guess I need to update it, but I don't want to buy the ridiculously expensive Shimano charger to plug it to the PC. Do I have another choice ? Is the charger only a charger or something more complex (eTube stuff) ?