Symptoms: No Gliffy diagrams can be searched. Type in "com.gliffy.core.integration.confluence.isGliffyDoc:true" without the quotes into Confluence Search.
This should return all gliffy diagrams, but 0 results are returned. User has already tested that the search index is fine (new diagrams can be searched). If search is broken for everything, try reindexing: https://confluence.atlassian.com/display/DOC/Content+Index+Administration
Solution: Check that the Lucene Compatibility Plugin is enabled. This is a system plugin in Confluence 5.2+ or a user plugin (brought in by us) in Confluence 5.1 and below. You can check this via Confluence Admin > Manage Add Ons > User Plugin or System Plugin > "Lucene Compatibility Plugin". Re-enable this plugin. Newly created diagrams will now be indexed. In order for older diagrams to show up you need to trigger a manual search re-index.