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Solution: The problem is not related to CONTROLLINO platform only. It seems to be a general weakness of Arduino IDE, avrdude and original bootloader. It is still not clear what exactly happens, but it seems that after upload of a corrupted binary the microcontroller skips the bootloader when reset during operation.
Are you sure it is not only Controllino issue, I have never had it with other Arduino-s…It happened again. This is ridiculous, we often need to change the code remotely, as the machine is far away – I cannot reset it remotely. I guess I cannot use this product for industrial machines as we hoped.