I guess that the Kindle generates those files after you sideload a book. Is there any way to remove this information from a book using Calibre?
Amazon purchased books get their .apnx wirelessly... so unless you leave the wireless off, it may get downloaded again.
For side-loaded books, calibre will automatically create a simulated .apnx file. If you go to Preferences->Plugins->Device interface plugins you can highlight the "Kindle 2/3 device interface", click the "Customize plugin button" and make sure those last two boxes are both unchecked:
"Send page number information when sending books"
"Use slower but more accurate page number generation"
Click apply (top left) and you're done. Calibre won't send the .apnx file when sideloading books to your Kindle anymore.