Maybe reset MKR1000 by clicking the blue button twice and program/install libraries again?
Honestly something like that is happening to me now. I bricked the MKR1000 and ordered a new one. I now reordered the shied because I think it bricked too. Fast Forward -- Now that the shield and MKR are working. I now think my encoders have blew out. I'm concluding that everything attached to the MKR1000 bricked/fried when I initially fried the board. I've re-ordered both [MKR1000, Motor Shield] and now about to re order the encoder. I'm working on the Arduino engineering kit lesson learned, I guess.
Full Disclosure: I had the components working with the encoder until I accidently plugged the lipo battery into the I2C headers. Lol, I don't know what I was thinkin. I guess brain exhaustion or lazy..
Unless someone tells me the encoder can't be bricked, because right now my encoder isn't working/stuck (won't rotate)