Answer
This usually indicates one or more Search Domains have become corrupted or have unsynchronized documents. In the Search Domains window in IEE, check which domains are active and whether any show unsynchronized documents; try synchronizing first, and if synchronization itself fails, drop and recreate the affected domain: RMB on it and choose 'Show Details', then from the detail view RMB and choose 'Drop Search Index'; refresh to confirm it's dropped; then RMB and choose 'Schedule Domain Activation', enable its schedule, run the resulting background job, and once it completes, resynchronize the domain the same way. Confirm success by checking the domain's 'Not Synchronized Documents' count reaches 0 afterward.