Updating metadata in the KF8 part of joint files is not supported. You can run a mobi to azw3 conversion. The azw3 will be updateable and you can send that to your kindle. Or you can use the tweak book function that will discard the non KF8 part leaving you with an updateable KF8 MOBI.
Notice to all: I can not
provide assistance with DRM removal, for legal reasons, so please do not contact me about it.