Stratix V Transceiver Reconfiguration issues

Oic, I just trying to understand your problem.

If you cannot recover the problem after the transceiver malfunction, then it seems like the reconfiguration affect some other bits.

Can you try one more experiment:

When it is working, try use serial loopback and check whether it works. Transceiver toolkit allows you to turn on serial loopback easily.

After that, when you perform reconfiguration and problem occurs, can you try to use serial loopback again?

This can isolate whether problem is due to your analog setting or problem in the reconfiguration process