Well, I came up with this solution by using Natron Python. It’s pretty straight forward and it works on my machine.
Go to Your Terminal( the following basically run natron in interactive mode with python interface)
${YOUR_NATRON_BIN_FOLDER}/Natron.exe -t
Once it finished loading bunch of stuffs. you will see >>> waiting for your input, now you execute following line by line.
NatronEngine.natron.getSettings().restoreDefaultSettings()
NatronEngine.natron.getSettings().saveSettings()
exit()
Now, you should be able to open Natron normally with default preferences. Hope this works on your machine.
Best,