If there are only 3 keys missing use SDS from the primary controller to sync those keys out to the resilient controller
The error you are getting normally occurs when, (1) there no more licenses or (2) someone has used the Opsman License on that controller which it uses for Resiliency. Mitel refer to this license as the hidden one.
However, it certainly should not say this if you are deleting.
What I do to fix this is to find a user or device that does not have the shared marks before the configeration line. This is an indicator that the extension was programmed on the system and not via opsman.