Settings are now stored in "NLCESettings.ini" to prevent clashes when loading settings. CE will initially read from "settings.ini" if it exists (to prevent you from having to do the config again), but will save to the new file and use that one from then on.
N.B. Both programs will continue to read/write to/from the same userdata.nxsv and hotkeys.ini. If running from the same directory, it's most likely that users will want this, since both programs will show the most up-to-date completion progress for all levels. As far as hotkeys are concerned, even if new ones are added to CE, NL would just ignore any lines it didn't recognise in hotkeys.ini.
N.B. Both programs will continue to read/write to/from the same userdata.nxsv and hotkeys.ini. If running from the same directory, it's most likely that users will want this, since both programs will show the most up-to-date completion progress for all levels. As far as hotkeys are concerned, even if new ones are added to CE, NL would just ignore any lines it didn't recognise in hotkeys.ini.