Glad to hear everything is working again. In the future you can check status.evernote.com to see the status of the service. Also you can always contact support at evernote.com/support with any issues you run into.
Thanks for the comments guys, I appreciate it. I use Evernote extensively both on OS X and Windows, and granted I don't merge notes that often, but it was an annoyance when the results weren't what I expected.