This is very normal wtih a kernel update. The kmod-nvidia-<kernel version> package is the one that is locally compiled and installed for the kernel version being removed when a new kernel is installed.
I have not seen this issue, but the config is not directly related to the nvidia driver. It is instead related to how the monitor edid is received and used when waking up from suspend.
I have not personally had issue, but there is information on troubleshooting resolution and refresh rates on several threads here. One recent one (found by a search for ‘edid’ ) is this one.