Before doing anything else, try editing the config file and removing the "LastSync" and "UnsyncedUrls" entries and then syncing again. It is possible that the device is only downloading a set number of articles. Removing these entries might let it download more. Alternatively, setting the timestamp for LastSync to something a long time ago might do it as well.
I doubt if editing the current database will get more articles downloaded. I think you would need to create entries for the missing articles. Without knowing what the articles where and the values needed, this would be impossible. You might be able to copy them from the backup database but it would take some experimenting to get it right.
For restoring the backup, I've done this plenty of times with no problems. Just remove all the files on the device and copy the backup files to the device. Then restart it after ejecting.
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