I have just found out the hard way that the Debian bug 854595 is a problem for us too: upgrading app-crypt/gnupg to the recently stabilised 2.1.18 has resulted in its scdaemon no longer being able to access keys stored in the OpenPGP applet of YubiKeys (tested on several YK4s). Downgrading to 2.1.15 (and killing scdaemon) makes things go back to normal. Please see the aforementioned Debian bug for a detailed description of symptoms.
Try with disable-ccid in scdaemon.conf and install app-crypt/ccid (killing scdaemon to ensure new drivers are used)
I see the same effect with the smart card reader in my Thinkpad T520, Bus 002 Device 004: ID 17ef:1003 Lenovo Integrated Smart Card Reader I have not tried k_f's advice yet, since I first went to the upstream bug. However, I can confirm that adding the two Debian patches from $URL to our 2.1.18 solves the problem for me, and I can access my card reader again.
For the record, at least in case of YK4 disabling the built-in CCID driver in favour of the external one does help.
(In reply to Marek Szuba from comment #3) > For the record, at least in case of YK4 disabling the built-in CCID driver > in favour of the external one does help. Also of interest is whether the issue persists in 2.1.19
Installing 2.1.19-r1 fixed the problem for me (YubiKey 4).
The relevant bug report seems below: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=852702 and the patch is here: https://anonscm.debian.org/cgit/pkg-gnupg/gnupg2.git/commit/?id=cd2ad84410ba2045338a30a15c1caa145335c445
(In reply to Diogo Pereira from comment #5) > Installing 2.1.19-r1 fixed the problem for me (YubiKey 4). Right, the mentioned patches are included in it so I'm not surprised. So if the workaround isn't sufficient I'd prefer stabilizing 2.1.19 rather than applying the specific patches.
Already stable on all but ia64, so closing this bug
