Ah, a dual-MOBI.
It has both KF8 and mobi7 sections, and your Paperwhite automatically uses the KF8 section.
Unfortunately, calibre does not support updating the KF8 metadata of a dual-MOBI (it's complicated).
Use
KindleUnpack or the linked calibre plugin to break it apart into its component AZW3 and MOBI, then send the AZW3.