I have eink Kobos and after comparing WiFi to Kobo and Download from Website to PC, I use download. To test I loaded into Calibre from the Kobo and also from downloaded ACSM file (or epub on DRM free titles).
I'm running Linux Mint with a Mate Desktop.
Years ago I had K4PC and the Sony Desktop on Windows. But I'd not bothered with the proprietary desktop applications even before switching from Windows to Linux.
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