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I was looking a little closer at that plugin. If you leave the custom column field blank in the device config, Calibre should generate its own page numbers regardless of whether the plugin is enabled or not. At least that is how it seems to be working here.
I created a custom column named pages and used the plugin to generate page counts for a few books. When I used the custom column (#pages) in the device config, the page count in the column was used. If a book didn't have a page count, Calibre generated its own page count when sending to the device--just as if the plugin wasn't installed.
I haven't done any tests with many books and am still not sure where things are going wrong for you. Try not restarting the kindle after removing/sending the books. I doubt that is causing problems but it would interrupt updates to the database which should continue after the restart... Not sure exactly.
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