I have the similar issue. Have you found the complete solution?
Simulink is unable to detect the MKR1000 after loading the program.
This the error which I am getting.
I also tried with Bootloader mode but no solution.
That is the error with Bootloader mode.
I also uninstalled the Arduino Support Packages and installed them again. But still not getting to the solution.
One thing which I want to mention here it that it is working fine in my another laptop. May be I should reinstall MATLAB!
It will be really appreciated if someone could guide me to the solution without uninstalling the MATLAB.
Atta ul Wasay