Access Denied on Affiliated content w/ Aggregation

Here is the situation: There are several domains aliasing to a single Drupal 6 installation (1 database, no prefixing). The site has been functioning properly for the past few weeks, aggregating feeds while it is developed. A confusing event occurred earlier in which the extra domain modules were mysteriously turned off and no one could figure out how it happened. (This is referencing Domain Alias, Domain Content, Domain Meta Tags, etc.... everything but the core and configuration modules.) The modules were turned back on and all settings were preserved with one apparent exception.

All content is now inaccessible by anonymous users. 'Access Denied' for everything. Everything was initially set up to publish to all domains but maintain a source domain. Well, the 'Publish to all domains' option is no longer checked on anything and editing the individual nodes by hand is inconceivable (there are over 13 thousand). All permissions have been verified, reset, rebuilt, verified yet again, and offered some tea, but to no avail.

First, does anyone know how we might be able to accomplish this in a batch operation?

Second, and what is frankly more important to me, does anyone have the foggiest idea just what the hell happened/is happening?