Deleting company-wide domains will remove the domain from all keystores associated with that company. Company-wide domains can be deleted only at the company level, not from individual keystores. If that company-wide domain is the only valid domain on a keystore, any devices with a valid configuration for that keystore will be able to pull a license from that keystore after it is deleted. Deleting company-wide domains will not affect any valid domains created directly on a keystore. If one exists, once the company-wide domain is deleted, devices will be able to access the keystore only if they are on one of the listed keystore-level valid domains.
Acme has a company-wide domain called "acme.com."
Acme has Keystore A and Keystore B. Keystore A and Keystore B will automatically receive "acme.com" as a valid domain.
Keystore B also has a valid domain of "roadrunner.com" that was defined for that keystore only. Therefore, Keystore A has "acme.com," and Keystore B has both "acme.com" and "roadrunner.com.'
If you delete the company-wide domain of "acme.com," Keystore A will be left with no defined valid domains. In other words, anyone with a valid configuration for this keystore will be able to access it. However, Keystore B will be left with the "roadrunner.com" valid domain, and so only a user on this domain will be able to access Keystore B (devices on the "acme.com" domain will no longer be able to access Keystore B, even if they have a valid configuration for this keystore).