If the liniar encoder is differential quadrature, you should be able to feed it directly to the CSMIO/IP-A encoder input. Motor encoder signals would continue to be fed directly to the servo drives, but would not be relayed to the CSMIO.
With this type of setup, you would implement the velocity loop within the servo drive, and the position loop within the CSMIO/IP-A.
I would add that I have no experience of doing this.
Allan