With default settings cross-platform agents in Operations Manager 2007 R2 don’t fail-over to another management server if the primary management server goes offline. If the primary management server goes offline you will loose monitoring of all cross-platform machines communicating through that management server. The System Center Cross platform and Interop team blog has a couple of scripts that can help you manage cross-platform machines. One of these scripts is used to to change the current management server monitoring a UNIX/Linux server (or group of UNIX/Linux servers) to a new management server.
But if you move a cross-platform over to another management server you will get an alert like this
A simple explanation to this is that the new management server don’t trust the CA which have issue the certificate that the cross-platform machine is communicating with. You can solve this by copy the certificate from the management server that first discover the cross-platform machine over to the second management server. Store the certificate under Local Computer/Trusted Root Certification Authorities (in the certificates MMC). The certificate is named SCX-Certificate, issued by the primary management server.
When the new management server has the certificate installed it will start communicate with the cross platform machine. You could build a timed script two state monitor to check if the first management server is working, else run the script to move all cross-platform agents.