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1) I'm sorry to tell you this, but syncing of sideloaded books is not something you can get back. Kobo has never offered that service. (I for one am grateful they don't; if I've sideloaded the book it's none of Kobo's business that I have done so.)
2) You don't need the Kobo app to sideload books, or any app except a file manager. Your Kobo should appear to your computer as a USB thumb drive. You can drag & drop book files to it.
3) The home screen shows a variety of different things, and can change a bit over time as you use the device. Mine, for example, shows my current reads at the top, then the row below it is split into "My Books" and my most-used collection. Now, I haven't gotten the latest firmware yet, so I suppose your home screen may be a bit different.
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