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Having the engine running is a lot different to just having the ignition switched on. When running, the ECUs are controlling the engine and therefore cannot be reset as required for any coding to take place. As suggested you could try loading backup files. You could also try disconnecting the battery for a short time so that all ECUs are be woken up again.
Sometimes when i code my car I notice that the head unit ecu does not show and i have to reconnect, sometimes more than once for it to show up.
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