Hi,
After you download the update package from NXP website and install, you 'd better to install one-by-one.
Some update will reset and could break others' installation which leads the missing packages.
https://www.nxp.com/webapp/swlicensing/sso/downloadSoftware.sp?catid=SW32K3-S32DS_3.4-D
Please login and download the update packages you want.
Cheers
Oliver