I was manually reindexing the search index using bin/search index --all, which resulted in the following error at 99.7% progress:
[2014-10-28 09:45:29] PHLOG: 'Unable to build document PHID-WIKI-amenci5bzyxy5k4ndwwu with indexer PhrictionSearchIndexer.' at [/home/tools/phabricator/phabricator/src/applications/search/index/PhabricatorSearchDocumentIndexer.php:64]
[2014-10-28 09:45:29] EXCEPTION: (Exception) Unable to load object by phid 'PHID-WIKI-amenci5bzyxy5k4ndwwu'! at [<phabricator>/src/applications/search/index/PhabricatorSearchDocumentIndexer.php:28]
#0 PhabricatorSearchDocumentIndexer::loadDocumentByPHID(string) called at [<phabricator>/src/applications/phriction/search/PhrictionSearchIndexer.php:11]
#1 PhrictionSearchIndexer::buildAbstractDocumentByPHID(string) called at [<phabricator>/src/applications/search/index/PhabricatorSearchDocumentIndexer.php:35]
#2 PhabricatorSearchDocumentIndexer::indexDocumentByPHID(string) called at [<phabricator>/src/applications/search/index/PhabricatorSearchIndexer.php:21]
#3 PhabricatorSearchIndexer::indexDocumentByPHID(string) called at [<phabricator>/src/applications/search/worker/PhabricatorSearchWorker.php:10]
#4 PhabricatorSearchWorker::doWork() called at [<phabricator>/src/infrastructure/daemon/workers/PhabricatorWorker.php:110]
#5 PhabricatorWorker::scheduleTask(string, array, integer) called at [<phabricator>/src/applications/search/index/PhabricatorSearchIndexer.php:11]
#6 PhabricatorSearchIndexer::queueDocumentForIndexing(string) called at [<phabricator>/src/applications/search/management/PhabricatorSearchManagementIndexWorkflow.php:92]
#7 PhabricatorSearchManagementIndexWorkflow::execute(PhutilArgumentParser) called at [<phutil>/src/parser/argument/PhutilArgumentParser.php:394]
#8 PhutilArgumentParser::parseWorkflowsFull(array) called at [<phutil>/src/parser/argument/PhutilArgumentParser.php:290]
#9 PhutilArgumentParser::parseWorkflows(array) called at [<phabricator>/scripts/search/manage_search.php:21]
We've been running this phabricator install for about 6 months now and never have changed anything by hand, e.g. in the database. The problem persists when running the search indexer a second time.