On the first business day of full Lync 2013 operations, some people were complaining they could not join meetings. When some users clicked on the Join Lync Meeting link in the email, they were greeted with a 404 - File or directory not found error in IE. If they tried several times, eventually they got in.
Further analysis showed that one specific front-end server was serving up the 404 errors, while the others were working fine. Thanks to the F5, we were able to easily remove that server from the load-balanced pool while we troubleshooted (troubleshot?) the problem.
The first thing to note about troubleshooting issues with the meet URL on an Enterprise Edition pool is that you can't connect directly to a specific server in a pool and expect to get the proper meeting join experience. For example, if your meet URL is meet.contoso.com and your Lync pool members are FE01.contoso.com, FE02.contoso.com etc, you would normally connect to a meeting via something like https://meet.contoso.com/user.name/FY3DFSE4. You can't troubleshoot issues with a specific server by connecting to https://FE01.contoso.com/user.name/FY3DFSE4. You'll get a 404 error, thanks to the way the URL Rewrite module processes URLs.
To get around this, you need to add a temporary HOSTS entry to your testing workstation for meet.contoso.com pointing to the server having the issue. This will bypass the load balancer and allow you to connect directly to the server you want to test.
Back to the problem....
After setting my HOSTS file to point directly to the "bad" server, I found I could browse to https://meet.contoso.com successfully, but not to a specific meeting like https://meet.contoso.com/user.name/FY3DFSE4, which threw a 404. Event logs didn't show anything wrong.
I'll spare you the hours of dead ends I tried and just give you the solution (because that's why you're here, right?)
I went to Control Panel and removed the IIS URL Rewrite Module 2. Then I re-ran Lync setup via the Lync 2013 Deployment Wizard, which re-added the URL Rewrite Module and reset the default URL rewrite rules Lync put in place. All this was done without reboots or service interruption. As soon as Lync setup completed, meeting joins happened without error.
So, it appears that something went wrong with one or more of the URL rewrite rules, which wasn't cleaned up by simply re-running Lync setup, or Enable-CSComputer, which was things other people suggested in various places I looked.
I hope this helps others who are having this issue.