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I accidentally deleted my /lib/modules/<kernel version directory>.

Here's the full output of sudo rm -rfv /lib/modules/4.14.98+ : pastebin

Is there a way to restore the modules keeping the system online?

It is a raspberry pi sitting on an internal network.

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You can use dpkg --search /lib/modules/<kernel version directory> to find what packages this directory (and inside) belong to, then use apt-get --reinstall install <list from before> to reinstall any affected package missing, thus restoring missing content.

In one liner this should be (remove the -d once sure of the effect):

apt-get -d --reinstall install $(dpkg -S /lib/modules/4.14.98+ | tr ',:' '\n\n' | head -n -1)

As I don't know well if RPi follows the usual kernel installation method (depmod etc.) you should then check that after this you can modprobe any random module (eg: the dummy module) not already loaded before considering everything is fine.

PS: in case of additional dkms modules, above won't track it, but you can then continue the "restoration" with dkms status to get a list and dkms install module/module-version -k 4.14.98+ to put back what's missing etc.

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