Maybe I'm not understanding your setup fully...
You have the Q03UDECPU and the MESIT module on the same rack but you're communicating over Ethernet instead of the back plane?
Also, according to Mitsubishi, the Ethernet port on any CPU is not intended for anything other than "Light" work. If you are using the port for large data transfers/communication you might want to consider a dedicated Ethernet module.
I'm assuming that when you way that you're loosing the network that the MESIT module is faulting out?
If that is the case you may need to look into your scan times, and use some on demand triggers.
As for t/s networking connectivity, if you have a manageable switch (sorry, didn't look up your model) you can mirror the ports and put Wire shark on it.
Just some brainstorm ideas here, disregard if I didn't understand your questions fully.