Ok, managed to do this. I had to copy again my entire library to a new device so I decided I could play around.
The _trick_, so to speak, is to sort the Calibre library in the order we want it copied in the device. I normally have the most recent books at the top, and that's what was screwing with my order. I sorted them so that the oldest ones were at the top, and then the modified date in the device fell where it should.
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