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Before upgrading with a new disk image, it is advised to backup the pypilot.conf file, and copy it back again. If you are upgrading through a package manager this is not an issue.
All of the pypilot settings are stored in a small text file pypilot.conf. This file is in json format and can be edited with a text editor.
simply copy this file somewhere before overwriting the disk image, and copy it back afterwards.
If you do not, it will be a fresh pypilot without calibration and you will need to perform all of these steps.