Problem:
When trying to compile a project using NanoPB, you see a warning like
MyProtocol.proto:11:27: Option "(nanopb)" unknown. Ensure that your proto definition file imports the proto which defines the option.
Solution:
At the top of the .proto file mentioned in the warning message, just after syntax = "proto3"; add the following line:
import "nanopb.proto";
After that, the error should be gone.