On all Kobo's I have worked with, once an ePub has been copied to the device, it is processed only once (at least, only once until the book is dropped; any re-adds of it will re-process the book).
My experience though has been with main-memory; not SD cards. Somewhere I do have a micro SD card but it's been AWOL for some time now. Maybe tis the time to get a new one and try some more experiments.
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