I tried that last night when it happened to me. Storing the performance did not restore the input, nor did changing the performance. Also, it happened after the unit had been one and I was running through performances. Issue occurred when I went from slot 4 to slot 5. After powering back on, no issues. Went back to same performance, same transition from slot 4 to slot 5 and no problem.
If it happens again I'll try to grab my laptop and hook up to rig manager. Maybe that would restore inputs somehow?