Large data downloads using neonUtilities may fail to download all available data due to the new API rate limit.
If your data download returns messages in the form "No files found for site SITE and month YYYY-MM", try downloading again, specifying only the sites and months that weren't found on the first attempt.
We are working to release a new version of neonUtilities that handles this situation smoothly. In the meantime, downloading small amounts of data and/or downloading using an API token will reduce the problem.