Does this only happen after an upload? What happens if you remove chassis and battery then put it back in, as is, without uploading?
Just so you know how the .ini files work, whenever you upload to your board it will ignore any saved files from an older upload, this includes the gestures.ini because the assumption is that you want to start with your new settings. So if it’s only happening after an upload then this is the cause and it’s intended to function that way.
If you want to change that behavior, you can keep your .ini settings active with the KEEP_SAVEFILES_WHEN_PROGRAMMING define BUT that applies to EVERYTHING and can cause changes in your config for presets or other defines to not show or work as expected so I highly recommend reading this page before you implement.