Unfortunately, there is an error in Kobo's syncing related to finishing a book. It probably isn't noticed when you have only one device and don't use any other Kobo app, but if you do, the finished status doesn't get synced properly.
While reading, the devices/apps will sync the current read status correctly. Sometimes it can seem a little slow, but that is usually because of when the last sync/refresh happened.
When you finish the book, this status change doesn't seem to get synced to the server. After a few syncs for each of the devices/apps, they will all show up as reading at 1%. Opening the book will start from the beginning. I'm pretty sure that if only one device/app is involved, the status stays correct on the device/app.
For this, the desktop application is just another app or device. It syncs to the server and gets the status. When you mark books as read, they should get marked as read on the device when you sync from the application. But, once a sync with the server happens, then this gets changed.
I'm not sure about the 99%. I don't used the desktop application enough to have seen this.
There is code in calibre to set the reading status based on a tag. But this is only done for very old firmware. This changed when the shelves/collections were added to the firmware. That was a long time before the Aura HD was released.
But, you can set the reading status from calibre using my Kobo Utilities plugin. This is one of it's many functions. There are several ways to do it. For books in the calibre library, you can use the metadata update function. Or from the device list, you use the "Change reading status" function. Or, you can use the "Store/Restore current bookmark" function. This can store the reading status of the books on the device and then later restore them. This will correctly set the status on the device if it changes.
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