I worked out how to use Adafruit color sensors with an i2c multiplexer. Class and example usage on github at https://github.com/Chris857/FTC-Code/tree/master/src/main/java/org/firstinspires/ftc/teamcode.
To use the example, create a configuration with two "I2C Device"s, named “ada” and “mux”. Edit the “ports” array to the ports on the multiplexer that you have color sensors plugged in to.