well the updates check mechanism checks \updates of each game, if you overwrite the original game files with the content of the downloaded update then it is not displayed. As long each game has a \updates dir and you (or the download via JNUStool) copy, for example v16 to this dir, by the next scan it will be visible. I hope this helps.. sorry english is not my native language.
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oh i get it, in the new beta3 i removed the Version column because normally this would not change and we all (could) have the same gamedisc rip. But.... If you have overwritten the game files with the content of the downloaded update then U-Indexer reads the meta.xml from the update and this version number is actually the update version number. Because i have removed this 'original version' column overwritten updaters (no offend) are no longer seeing any version difference. Overwriting your original gamefiles with updates on HD is not smart, if you need a rollback, because the latest update contains SD card detection or so you have to to download the whole game again, on SD card it is handy to save space i agree. So stick with \updates method like loadiine uses and as a bonus my tool will assist you with signalling, downloading and copying.
Example: if you conform to \updates mechanism
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v192 update of splatoon was installed in \updates of gamedir, but my tool signals that v224 is available, and you can then download it with JNUStool and afterwards u-indexer can copy it to the correct gamedir. After a new scan both updates would be shown and you can of course delete the older update after testing.