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The Quality Check plugin has an option to update the ebook file sizes in calibre.
If you don't want a plugin, another option might be to delete the PDF format only from the calibre record, leaving the metadata intact, then add the smaller PDF file back in. I would expect calibre to refresh it's file size here.
The easiest way to do that is using the detail panel on the right edge of the calibre window: right click on the PDF there, and choose the option to delete that format from calibre. Then, from your file browser, drag the updated PDF into the detail panel to add the new PDF format back in.
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