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The new kernel packages will still be installed. You can change the default kernel yourself via /etc/grub.conf. You will have to rerun the NVIDIA installer any time you change the kernel version.
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Note: it may be possible to use DKMS with the nvidia module so it gets built automatically. SCS has not tested this. See this README which suggests that DKMS could be used:
ftp://download.nvidia.com/XFree86/Linux-x86/381.09/README/installdriver.html
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