I am testing some of my digital compasses by placing them in a dycome. I'm using I2C to communicate with the compasses so I will need to keep the Arduino relatively close to the sensor, which means it will be in the dycome with the magnetometer.
Is there any reason I should not do this? I will only be applying a magnetic field strength up to 400mG.
But due to EMI, the board or the sensor could hang:
Consider 10 or 20 ohm series resistors ( you can try up to 120 ohm) between the Due and the bus (one for SDA, another for SCL). This will attenuate the glitches leaving your Due, and eventually detect timeouts to reset the I2C bus if necessary. You will find a I2C bus reset function in the DUE sub forum.
A dycome is a machine that lets you apply a magnetic field in any direction you want, including inclination. I don't think they're very common anymore but they're useful for testing magnetometers.