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Posted
21 minutes ago, bigbangatk said:

How do I use batch editor to edit pokemon in a specific box?

Drag all the pokemon in that box to another PKHeX window
perform your batch edit on the other PKHeX window
Drag the pokemon back into your save.

(you can also use the import/dump box feature)

 

edit.
Apparently as seen on the batch editor guide page (which I know you've seen), there is a box function.

You could try:
=Box=1     (when box is box 1)
insert your code here

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