mod_rewrite stopped working

In one of my domains, mod_rewrite suddenly stopped working. Before when someone went to [urlroot]/wpmultisitename, they would be taken to the appropriate person's Wordpress Multisite. Now, when someone goes to [urlroot]/wpmultisitename, they get a file not found error.

We don't know of anything specific that triggered it. It just stopped working. We can use a .htacess file to do the rewrites, but none of the rewrites set in EHCP appear to be having any effect.

One reason that we're having difficulty troubleshooting this is that it is difficult to tell what files are governing mod_rewrites. We've been able to establish that mod_rewrite is on, but we can't tell if it's running the rewrite commands that we think it's running or some other set elsewhere on the computer. We're using Ubuntu, so the default location is /etc/apache2/sites-available/default, but this does not contain the commands that are set through EHCP.

How, in general, do mod_rewrites work in EHCP-managed domains, and how can we figure out what the problem is?

Thank you,