HID advises users to take the following steps to mitigate these threats.

Protect your reader configuration cards.

A malicious encoder or reader must be physically close to the reader configuration cards to communicate with them and extract information. Elite Key and Custom Key users that have kept their configuration cards secure should continue to be vigilant and restrict access to those cards.
HID standard key users and other users 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.

Protect your credentials and disable legacy technologies.

Reading the PACS data from a credential is not enough to clone the credential for modern technologies like Seos and DESFire. These technologies use a credential key for authentication. However, if a system's readers still support legacy technologies (i.e., HID Prox, MiFARE Classic, etc.), then it may be possible to insert the credential information into a legacy technology credential that would be accepted by those readers. Users are encouraged to disable legacy credential technologies in their readers.
Further, physical credentials should always be kept safe by their users, and site managers should remind their users to be vigilant with their credentials and report missing or stolen cards.

Harden your iCLASS SE Readers from configuration changes

iCLASS SE Readers using firmware firmware version 8.6.04 or higher can use the HID Reader Manager application to prevent the readers from accepting configuration changes from configuration cards. After this is complete, users may then securely destroy their reader configuration cards.
If you need assistance, or if the reader firmware has not been updated to 8.6.04 or higher, contact HID Technical Support.

Harden your HID OMNIKEY Readers, HID iCLASS SE Reader Modules, HID iCLASS SE Processors from configuration changes

Contact HID to receive a "Shield Card" that will prevent further configuration changes using reader configuration cards. After this is complete, users may then securely destroy their reader configuration cards.

Omnikey 5427Ck Firmware Security Vulnerabilities