I often read the same book on both of my Kobos, but I never sync and sideload everything, so it doesn't matter where I bought the book. I edit the css and the metadata, so I never read any direct downloads even when I bought the book from Kobo. It's not that hard to find my place manually.
I used to read direct downloads and sync 10-12 years ago, but the inconsistent formatting and metadata bothered me so much that I stopped doing it pretty quickly. I started to fix everything in Calibre and never looked back.
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