There a is a issue I am having for quite a long time I hadn't been able to quickly solve, so I just sucked it up. The issue is, that if I plug off the Yubikey off the laptop's USB port, one CPU goes haywire 100% usage and some, but not all services or applications that require internet access cannot reach it.

The issue resolves itself when the Yubikey is plugged back into the USB port or the pcscid.service is restarted:

sudo systemctl restart pcscid.service

There is nothing relevant I could find in dmesg output, probing journal:

journalctl -xeu pcscid.service

There is something, but with my current understanding this is not of much help, still keeping it here for searching:

Dec 17 10:42:42 peterbabic pcscd[600525]: 99999999 ccid_usb.c:899:WriteUSB() write failed (1/45): LIBUSB_ERROR_PIPE
Dec 17 10:42:42 peterbabic pcscd[600525]: 00000037 ifdwrapper.c:364:IFDStatusICC() Card not transacted: 612
Dec 17 10:42:42 peterbabic pcscd[600525]: 00000010 eventhandler.c:336:EHStatusHandlerThread() Error communicating to: Yubico YubiKey OTP+FIDO+CCID 00 00
Dec 17 10:42:42 peterbabic pcscd[600525]: 00479093 ccid_usb.c:899:WriteUSB() write failed (1/45): LIBUSB_ERROR_NO_DEVICE
Dec 17 10:42:42 peterbabic pcscd[600525]: 00000062 ccid_usb.c:1501:InterruptRead() libusb_submit_transfer failed: LIBUSB_ERROR_NO_DEVICE

The most common recommended solution appears to be:

echo "disable-ccid" >> ~/.gnupg/scdaemon.conf

I was quite surprised I did not have it there, because last December I personally wrote a post suggesting to insert it there.

So I (re-)inserted the config option into the file and now I wait and observe what will be going on. Adding a list of open links to the bottom because I feel I will need to get back to this in the future.