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I studied this problem later and found that this is not completely answered. Arduino is a very limited platform and cannot operate at micro seconds level for communicating with the ROS master. It is due the AVR limitations. My project I got a maximum of 30Hz for sending the rotary encoder data and receiving the motors commands. I wish I could go to something closer to the MHz level.

IMUs are also another big issue, I cannot operate a High end IMU, because AVR is too slow.

So for other people also losing connection with the Arduino or having delay happening when communicating with Arduino. Now you know that Arduino is fairly limited and running Timers on the code, and using ROS Throttle is the way to fix.

I would love to hear if someone has some high end PIC or FPGA ready to apply and easy to use as Arduino.