Yes, you can run multiple CA servers that belong to different organizations in the same blockchain, provided that the cacerts directory of the MSP directory contains the certificate authority chains of other certificate authorities which represents the roots of trust for the peer.
To do these, you have to first initialize your CA server and after that, you can get the root certificates using the
The fabric-ca-client getcainfo command is used to retrieve these certificate chains from other
Fabric CA server instances.
For more information, check out the following link.