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Your assumption is correct.
I have a copy of everything I've ever put on my EE on our FTP server (normal PC for most people) so your idea of copying everything via USB should work unless you have made extensive notations to your books, in which case you need to check the old edge archive for ways to back that up and what files are involved.
If you don't have notations then the simple copy should be all you need.
When you upgrade check all the usual pitfalls before you start:
The downloaded update zip file is not corrupt - check by opening it on the PC
Update file named to update.zip - take care that it isn't .zip.zip
USB stick is a small capacity and formatted FAT or FAT32
The update.zip is in the root directory of the USB stick
The PE is fully charged and plugged in to the charger
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