HID Global recommends the following mitigations to reduce the risk:

Elite Key and Custom Key customers that have kept their configuration cards secure should continue to be vigilant and restrict access to those cards. To exploit this vulnerability, a reader must be physically close to or in possession of the configuration cards to communicate with the card and extract information.
Administrators should plan to securely destroy unneeded configuration cards.
Customers using the HID standard key, and other customers who are concerned their keys may be compromised should consider steps to update the readers and credentials with new keys. To assist in this effort, HID will be introducing a free upgrade to the Elite Key program. Contact your HID representative for more information at https://www.hidglobal.com/support.

HID has also provided additional steps users can take steps to harden their readers to prevent malicious configuration changes.

iCLASS SE Readers

iCLASS SE Readers using firmware version 8.6.0.4 or higher can use the HID Reader Manager application to prevent the readers from accepting configuration changes from Configuration Cards.
If you need assistance, or if the reader firmware has not been updated to 8.6.0.4 or higher, contact HID Technical Support.

HID OMNIKEY Readers, OMNIKEY Secure Elements, iCLASS SE Reader Modules, iCLASS SE Processors

Contact HID to receive a "Shield Card" that will prevent further configuration changes using reader configuration cards.

Iclass Se Reader Configuration Cards Firmware Security Vulnerabilities