Hello
I have the same exact same Issue here and I’m in cubase pro 10.0.20 Build 187
Impossible for every midi track associated with an Instrument track to recover their output after disabling/enabling the related instrument track.
I was so happy to built a bigmockup and then saving memory by disabling every temporary not needed instruments Butwith taht issue… I’m so disapointed… 
Running A Mac OS Sierra MacPro 10.12.6
2 x 2,93 GHz 6-Core Intel Xeon
Thanks for having reported it in Cubase 9.5, Should I also report it for the v10 ?
Best
Nicolas