diff --git a/src/graph/graphAdjacencyIndex.ts b/src/graph/graphAdjacencyIndex.ts
index bf0963af..af58c5cf 100644
--- a/src/graph/graphAdjacencyIndex.ts
+++ b/src/graph/graphAdjacencyIndex.ts
@@ -568,6 +568,8 @@ export class GraphAdjacencyIndex {
       // Clear current index
       this.verbIdSet.clear()
       this.totalRelationshipsIndexed = 0
+      // v6.2.4: CRITICAL FIX - Clear relationship counts to prevent accumulation
+      this.relationshipCountsByType.clear()
 
       // Note: LSM-trees will be recreated from storage via their own initialization
       // Verb data will be loaded on-demand via UnifiedCache
diff --git a/src/utils/metadataIndex.ts b/src/utils/metadataIndex.ts
index 70223374..b0b92105 100644
--- a/src/utils/metadataIndex.ts
+++ b/src/utils/metadataIndex.ts
@@ -381,6 +381,12 @@ export class MetadataIndexManager {
    */
   private async lazyLoadCounts(): Promise<void> {
     try {
+      // v6.2.4: CRITICAL FIX - Clear counts before loading to prevent accumulation
+      // Previously, counts accumulated across restarts causing 100x inflation
+      this.totalEntitiesByType.clear()
+      this.entityCountsByTypeFixed.fill(0)
+      this.verbCountsByTypeFixed.fill(0)
+
       // v6.2.2: Load counts from sparse index (correct source)
       const nounSparseIndex = await this.loadSparseIndex('noun')
       if (!nounSparseIndex) {
@@ -2501,6 +2507,13 @@ export class MetadataIndexManager {
       this.fieldIndexes.clear()
       this.dirtyFields.clear()
 
+      // v6.2.4: CRITICAL FIX - Clear type counts to prevent accumulation
+      // Previously, counts accumulated across rebuilds causing incorrect values
+      this.totalEntitiesByType.clear()
+      this.entityCountsByTypeFixed.fill(0)
+      this.verbCountsByTypeFixed.fill(0)
+      this.typeFieldAffinity.clear()
+
       // Clear all cached sparse indices in UnifiedCache
       // This ensures rebuild starts fresh (v3.44.1)
       this.unifiedCache.clear('metadata')