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The MD5 sum in the message definition is how ROS checks that message formats match. Messages with MD5 sums that don't match don't have the same format or the same serialization, and if you try to force them to be used together by editing the MD5 sums to match, you will get garbled or corrupt data.

If you change the message definitions that are used by your arduino, you should run to regenerate the ROS arduino libraries, and then rebuild your arduino project and flash it again.

And as you already know, if you change the message definitions you also need to run catkin_make to recreate C++ and python libraries and recompile anything that uses them on the host side.