Not sure why the indexer wouldn't pick these up.  Here's some code to reindex everything:

ArrayList array = new ArrayList();
IList pages = new EPiServer.DataAccess.PageListDB().ListAll();
foreach (EPiServer.Core.PageReference page in pages)
     array.Add(page.ID);
 
IndexPageJob job = new IndexPageJob((int[])array.ToArray(typeof(int)));
job.Execute();

Put that in a Scheduled Job and run it.  (Alternately, I guess, you could just re-save all the pages programtically, but this would probably be less overhead.)

That's from Mari, over in this thread, which is probably worth reading too.

Thanks Deane. Ill try that.