I'll keep this on needs triage because I don't know what the issue could be. I have a yubikey 5 at hand and just tested it with Gpg4win 3.1.11. It works without problems.

Can you please enable scdaemon debugging (Kleopatra settings -> GnuPG System -> Debug-Level 4 ( all ) ) and look at the log / attach it here.

Please, note the following uncommon behavior:

1. Set the debug mode as advised, but Yubikey was not recognized in Kleopatra or by command line and log file remained empty (0 Byte), see screenshots pages 1-4 sent by e-mail to you.

2. I inserted afterwards a smart card, in the command line the smart card was found, but not in Kleopatra, see page 5 of the screenshots attached.

3. I did a reboot and inserted a smart card (the same card as under (2), the card could be read by command line and by Kleopatra. Afterwards I connected the Yubikey. Not identified at all. If I entered: gpg --card-status (the Yubikey was fixed and the smart card removed), it showed the removed smart card data in the command line window. From test (3) I was able to get a scdaemon_log (attached), but I assume the data written in is only from the smart card, not from the Yubikey.

So long, as I only use smart cards, it works fine with gpg. If I insert a Yubikey, the system is out of order until I reboot. The "disorder" affects only smart card & Yubikey detection in gpg. All other programs are working fine!

It should be mentioned, that the notebook has an integrated smart card reader, a Reiner sct comfort smart card reader with PIN pad can be connected and Yubikeys. I using quite often smart cards (also by authentication for Bitlocker encryption and in some apps, e.g. qualified signatures, all this is working).

Both Yubikey working fine outside gpg / ssh. I can use it for OTP, U2F and Yubico apps working as well.

I appreciate your support in this matter, because I lost little bit the bearing by this problem and Yubico support does not answer at all.

Maybe a silly question, but let's be sure: Is the Openpgp app enabled on that Yubikey and is it enabled for usb? I can't remember the Yubikey commands on how to check this but tehre should even be a GUI. These days I use the new gpg-card tool to manage my Yubikeys (from GnuPG master).

if you want to give it a test on the command line, make sure that scdameon is not running and then run

scdaemon --log-file - -v --server

and enter

serialno openpgp

on the console. Any error messages?

Werner, no silly questions exist, only silly answers are existing. However, Yubikey is enabled for usb. I using Yubikey Manager a GUI, for the USB interface it is enabled: OTP, FIDO, FIDO U2F, OpenPGP, PIV and OATH. Thanks also for the suggested command line test. Indeed an error code shows up:

2020-01-12 15:49:04 scdaemon[15924] Handhabungsroutine für fd -1 gestartet
OK GNU Privacy Guard's Smartcard server ready
serialno openpgp
2020-01-12 15:49:24 scdaemon[15924] detected reader 'Microsoft IFD 0'
2020-01-12 15:49:24 scdaemon[15924] detected reader 'Yubico YubiKey OTP+FIDO+CCID 0'
2020-01-12 15:49:24 scdaemon[15924] detected reader ''
2020-01-12 15:49:24 scdaemon[15924] reader slot 0: not connected
2020-01-12 15:49:24 scdaemon[15924] pcsc_connect failed: removed card (0x80100069)
2020-01-12 15:49:24 scdaemon[15924] reader slot 0: not connected
ERR 100696144 No such device <SCD>

Hope, it is helpful for you to find the root cause.

At least one configuration error I could identify by myself: Kleopartra -> GnuPG-System -> Smartcard -> Connecting Reader with port N. If it is written: Yubico YubiKey OTP+FIDO+CCID 0 then Yubikey is recognized. I forgot to write "Yubico Yubikey" at the beginning and the "0" at the end. Now smart cards and Yubikeys are working for gpg. What is still a problem is SSH. A SSH key is on smart card or the Yubikey.

PuTTY generally work with SSH keys, so long as the SSH key is on a USB stick. Because in this particular case I can enter a path to the USB stick in "Options controlling SSH authentication: Private Key File for authentication". I can browse the path to the USB stick and can find the private SSH key there. In case of a smart card or Yubikey I cannot enter the path to the smart card or Yubikey. Most probably another silly configuration problem. However, I appreciate your comments!