Calibre will not be adding those page numbers - they must be in the original file! That implies the LRF itself was converted from some other format as it is not normal to have page numbers in a LRF file.
You might be able to use the Search/Replace facility in conversion to remove them. This would involve working out a suitable regex expression to identify them, so if you are not familiar with regex you should read the tutorial to get an idea of what to do. Then you can use the wizard on the regex search/replace dialog to see what the input would look like at the point the regex would have to operate.
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