Your printer has a controller board that resets on a new connection via the serial interface. A lot of them if not the majority do. There's nothing OctoPrint can do about that, it's a "feature" of your printer's hardware.
Since OctoPrint can't query the printer status without connecting to it, it also can't warn you about that before you hit connect (and displaying a warning every time you hit connect would be incredibly annoying to the majority of users who don't run SD prints outside of OctoPrint's control).
Nonetheless, the following works for some boards:
stty -F /dev/ttyACM0 -hupcl
which will disable "the usual" USB -> Serial -> CTS/DTR, etc -> RESET action
Same issue and even cut the 5V USB line from the Pi to the 2560 board.
After that, the Pi would not connect to the 2560, but found another post saying that the 2560 needs power on that 5V USB line, and to power it from the Ramps board. Tried that and it worked.
The 2560 still resets if I have to reconnect after starting a print.
Is the suggested command above ( stty -F .... ) something that is run in OctoPrint browser before connecting, or run when connected to the Pi using Putty ?
And does it need to be run every time a connection needs to be made without resetting the 2560, or is this a 'run once and saved on the Pi even if Pi is shut down and restarted' ?
Regarding your question, as far as I understand how stty works you'd need to run this after every reboot of the Pi/physical reconnect of the printer. You might have luck with a custom udev rule maybe?
But someone who actually uses this might want to correct me here, I merely copied this from the old FAQ here.
