?
We were planning to remove the filewatcher entirely in a future version. For now, we have added a UseFileSystemWatcher setting on the Admin->All Settings page. If you set this to False, and then restart the ProGet service, it will not use the watcher at all. Instead, it will check for updated files at the interval in the FeedIndexerThrottle setting (which by default is 60 seconds).
Our best guess is that the internal buffer on the filewatcher was overflowing due to the large number of files, causing this strange behavior. Let us know if this helps. v3.1.5 with this workaround has been released.