Which TwinCAT version did you use in your case?
I can acknowledge that the boot project is missing (or not the latest one) with TwinCAT 3.1.4022 when this dialog appears: "The application 'Port_851' is currently in RUN mode on the PLC. However, do you want to download the latest code changes?"
With TwinCAT 4020.28 and 4024 I can't remember any case with missing or old boot project.
Further feedback/experiences are welcome.
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