Lets look at it from a purely electrical standpoint. I won't go into the Superconductor physics, as I'm no expert in that field. The equivalent circuit of a standard transformer is as follows. The values of the secondary are transformed to the primary side. (the \$R_{\sigma}\$ can be ommited completely as it is a representation of iron losses that we don't have here)

simulate this circuit – Schematic created using CircuitLab
This figure represents a classic transformer. You suggest that we remove \$R_{prim}\$, \$R_{\sigma}\$ and \$R_{sec}\$. If we do so we are left with a simpler circuit with only inductances and the resistance of the load.

simulate this circuit
Solving the circuit shouldn't be a problem for you I guess. Find the stationary values of the currents in this regime. You have now found your initial conditions for the circiut in the first schematic.
Explanation: You calculated the currents \$ I_{prim}, I_{sec} \dots \$ these currents will flow while the material is a superconductor. When it changes to a normal conductor, the currents will still be there. These currents are therefore your initial conditions for the network that has resistances(non superconducting superconductors).
The thing you need to do is calculate all of the parameters and solve these two networks. When you do that you will see if your transformer will evaporate from the transition strain :-)
EDIT: Another thing comes to mind. The exact point in time when they loose their superconductivity is important(sin goes from -1 to 1). There is probably even a optimal sequence for getting them to the non-superconduting state based on the phase difference.
I hope that my explanation makes sense!
Cheers