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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.
I have imported most of my pages in my episerver cms 6 site with the "import data"-function. The content of the imported pages isn't searchable. If I in Edit Mode mark a page as "Mark page as changed" or changes anything else and save/publish the content becomes searchable. Is there any way to make the imported pages searchable directly?