My guess is as well, that OpenSC is claiming the device.
@nitroalex Can you investigate, how to disable it, without hurting the GnuPG use? I have tried with:
sudo systemctl stop pcscd
sudo systemctl mask pcscd
but turns out GnuPG uses pcscd as well (on Fedora 29), and this results in GnuPG not working anyway in my brief tests.
@Budgie2
Please use this script as a workaround (works for me on F29):
#!/bin/bash
date
sudo killall pcscd scdaemon
while ! gpg2 --card-status; do sudo killall pcscd scdaemon; echo "."; sleep 1s; done