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It should happen automatically given two prerrequisites:
1. KOReader knows about the specific library you're pushing books to.
2. Your computer and your device share time and timezone (which should be granted on sane devices but not on kindles).
If your on-device collection isn't very large and/or your device is powerful/recent enough you can make sure you're always consuming on-device latest metadata by disabling cache in the calibre plugin settings, within KO.
The reason of the behaviour you saw can be probably explained like that: during that timeframe (3h) your cache was "newer" than the metadata itself, so it was used. After that time a new search will figure out the metadata is newer than the cache and trigger a rebuild.
tl;dr: on most devices it should work out of the box. on kindles the easiest workaround is to disable cache.
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