I have Yubikey with the firmware version 1.0.8.
Its ATR announces "unknown" for support of TERMINATE_DF/ACTIVATE, so, "factory-reset" command of gpg frontend doesn't work.
And for newer version (4.2.7, which I don't have) it seems that it is supported, but it goes into terminated state (and not activated).
Both cases, the method in the page at Yubico works:
https://developers.yubico.com/ykneo-openpgp/ResetApplet.html