Gilbert, you can reindex all of your content by running search_observer__enqueue sql function with UPDATE. The "problem with the search indexer" seems to be related with content stored as a file or lob, right (therefore, you would need db_blob_get)? I clearly remember testing it for all types of storage, so it's a bit of a surprise that you see this problem.
I don't expect that the tree_sortkey change affected the search package in any way. It's probably what Don described in his reply to your message. I can't test this right now, so I would appreciate if you could try to add a db_transaction around db_blob_get and let us know of the outcome.
