diff --git a/boltz/crud_test.go b/boltz/crud_test.go
index 65eb788..0f2f5b6 100644
--- a/boltz/crud_test.go
+++ b/boltz/crud_test.go
@@ -403,6 +403,16 @@ func TestSetIndex_CheckIntegrity(t *testing.T) {
 	expectedMsg := "for index on employees.roleAttributes, val bash references id invalid, which doesn't exist"
 	test.requireIntegrityErrorAndFixResult(test.empStore, expectedMsg, true)
 
+	err = test.db.Update(func(tx *bbolt.Tx) error {
+		index := test.empStore.indexRoles.(*setIndex)
+		indexBucket := Path(tx, index.indexPath...)
+		return indexBucket.GetOrCreateBucket(string("bash")).GetError()
+	})
+	test.NoError(err)
+
+	expectedMsg = "for index on employees.roleAttributes, index value bash has no referenced values"
+	test.requireIntegrityErrorAndFixResult(test.empStore, expectedMsg, true)
+
 	err = test.db.Update(func(tx *bbolt.Tx) error {
 		index := test.empStore.indexRoles.(*setIndex)
 		indexBucket := Path(tx, index.indexPath...)
diff --git a/boltz/indexes.go b/boltz/indexes.go
index 1cc95ab..bb4c42b 100644
--- a/boltz/indexes.go
+++ b/boltz/indexes.go
@@ -269,6 +269,7 @@ type SetReadIndex interface {
 
 type Constraint interface {
 	Checkable
+	Label() string
 	ProcessBeforeUpdate(ctx *IndexingContext)
 	ProcessAfterUpdate(ctx *IndexingContext)
 	ProcessBeforeDelete(ctx *IndexingContext)
@@ -281,6 +282,10 @@ type uniqueIndex struct {
 	indexPath []string
 }
 
+func (index *uniqueIndex) Label() string {
+	return fmt.Sprintf("unique index on %s.%s", index.symbol.GetStore().GetEntityType(), index.symbol.GetName())
+}
+
 func (index *uniqueIndex) Read(tx *bbolt.Tx, val []byte) []byte {
 	indexBucket := index.getIndexBucket(tx)
 	if indexBucket.Err != nil {
@@ -428,6 +433,10 @@ type setIndex struct {
 	listeners []SetChangeListener
 }
 
+func (index *setIndex) Label() string {
+	return fmt.Sprintf("set index on %s.%s", index.symbol.GetStore().GetEntityType(), index.symbol.GetName())
+}
+
 func (index *setIndex) AddListener(listener SetChangeListener) {
 	index.listeners = append(index.listeners, listener)
 }
@@ -560,6 +569,9 @@ func (index *setIndex) ProcessBeforeDelete(ctx *IndexingContext) {
 		for _, val := range values {
 			indexBucket := index.getIndexBucket(ctx.Tx(), val.Value)
 			ctx.ErrHolder.SetError(indexBucket.DeleteListEntry(TypeString, ctx.RowId).Err)
+			if k, _ := indexBucket.Cursor().First(); k == nil {
+				ctx.ErrHolder.SetError(index.deleteIndexKey(ctx.Tx(), val.Value))
+			}
 		}
 	}
 }
@@ -590,11 +602,16 @@ func (index *setIndex) deleteIndexKey(tx *bbolt.Tx, key []byte) error {
 func (index *setIndex) CheckIntegrity(ctx MutateContext, fix bool, errorSink func(error, bool)) error {
 	tx := ctx.Tx()
 	if indexBaseBucket := Path(tx, index.indexPath...); indexBaseBucket != nil {
+		var toDelete []string
 		cursor := indexBaseBucket.Cursor()
 		for key, _ := cursor.First(); key != nil; key, _ = cursor.Next() {
+			hadRefs := false
 			if indexBucket := indexBaseBucket.Bucket.Bucket(key); indexBucket != nil {
 				idsCursor := indexBucket.Cursor()
+				referenceCount := 0
 				for val, _ := idsCursor.First(); val != nil; val, _ = idsCursor.Next() {
+					hadRefs = true
+					referenceCount++
 					_, id := GetTypeAndValue(val)
 					if !index.symbol.GetStore().IsEntityPresent(tx, string(id)) {
 						// entry has been deleted, remove
@@ -602,6 +619,7 @@ func (index *setIndex) CheckIntegrity(ctx MutateContext, fix bool, errorSink fun
 							if err := idsCursor.Delete(); err != nil {
 								return err
 							}
+							referenceCount--
 						}
 						errorSink(errors.Errorf("for index on %v.%v, val %v references id %v, which doesn't exist",
 							index.symbol.GetStore().GetEntityType(), index.GetSymbol().GetName(),
@@ -621,6 +639,7 @@ func (index *setIndex) CheckIntegrity(ctx MutateContext, fix bool, errorSink fun
 								if err := idsCursor.Delete(); err != nil {
 									return err
 								}
+								referenceCount--
 							}
 							errorSink(errors.Errorf("for index on %v.%v, val %v references id %v, which doesn't contain the value",
 								index.symbol.GetStore().GetEntityType(), index.GetSymbol().GetName(),
@@ -628,6 +647,15 @@ func (index *setIndex) CheckIntegrity(ctx MutateContext, fix bool, errorSink fun
 						}
 					}
 				}
+				if referenceCount == 0 {
+					if fix {
+						toDelete = append(toDelete, string(key))
+					}
+					if !hadRefs {
+						errorSink(errors.Errorf("for index on %s.%s, index value %s has no referenced values",
+							index.symbol.GetStore().GetEntityType(), index.GetSymbol().GetName(), string(key)), fix)
+					}
+				}
 			} else {
 				// If key has no values, delete the key
 				if err := cursor.Delete(); err != nil {
@@ -635,6 +663,12 @@ func (index *setIndex) CheckIntegrity(ctx MutateContext, fix bool, errorSink fun
 				}
 			}
 		}
+
+		for _, deleteKey := range toDelete {
+			if err := indexBaseBucket.DeleteBucket([]byte(deleteKey)); err != nil {
+				return errors.Wrapf(err, "error deleting unused key %s from index %s", deleteKey, index.Label())
+			}
+		}
 	}
 
 	for idsCursor := index.symbol.GetStore().IterateValidIds(tx, ast.BoolNodeTrue); idsCursor.IsValid(); idsCursor.Next() {
@@ -670,6 +704,12 @@ type fkIndex struct {
 	nullable bool
 }
 
+func (index *fkIndex) Label() string {
+	return fmt.Sprintf("fk index %s.%s -> %s.%s",
+		index.symbol.GetStore().GetEntityType(), index.symbol.GetName(),
+		index.fkSymbol.GetStore().GetEntityType(), index.fkSymbol.GetName())
+}
+
 func (index *fkIndex) ProcessBeforeUpdate(ctx *IndexingContext) {
 	if !ctx.ErrHolder.HasError() {
 		_, fieldValue := index.symbol.Eval(ctx.Tx(), ctx.RowId)
@@ -828,6 +868,12 @@ type fkDeleteConstraint struct {
 	fkSymbol EntitySymbol
 }
 
+func (index *fkDeleteConstraint) Label() string {
+	return fmt.Sprintf("fk delete contraint %s.%s -> %s.%s",
+		index.symbol.GetStore().GetEntityType(), index.symbol.GetName(),
+		index.fkSymbol.GetStore().GetEntityType(), index.fkSymbol.GetName())
+}
+
 func (index *fkDeleteConstraint) ProcessBeforeUpdate(_ *IndexingContext) {
 }
 
@@ -870,6 +916,11 @@ type fkConstraint struct {
 	nullable bool
 }
 
+func (index *fkConstraint) Label() string {
+	return fmt.Sprintf("fk constraint %s.%s",
+		index.symbol.GetStore().GetEntityType(), index.symbol.GetName())
+}
+
 func (index *fkConstraint) ProcessBeforeUpdate(ctx *IndexingContext) {
 	if !ctx.ErrHolder.HasError() {
 		_, fieldValue := index.symbol.Eval(ctx.Tx(), ctx.RowId)
@@ -944,6 +995,11 @@ type fkDeleteCascadeConstraint struct {
 	cascadeType CascadeType
 }
 
+func (index *fkDeleteCascadeConstraint) Label() string {
+	return fmt.Sprintf("fk delete cascade index %s.%s",
+		index.symbol.GetStore().GetEntityType(), index.symbol.GetName())
+}
+
 func (index *fkDeleteCascadeConstraint) ProcessBeforeUpdate(*IndexingContext) {
 }
 
diff --git a/boltz/store_crud.go b/boltz/store_crud.go
index 0bddb23..9cf8843 100644
--- a/boltz/store_crud.go
+++ b/boltz/store_crud.go
@@ -18,6 +18,7 @@ package boltz
 
 import (
 	"github.com/google/uuid"
+	"github.com/michaelquigley/pfxlog"
 	"github.com/openziti/foundation/v2/errorz"
 	"github.com/openziti/foundation/v2/stringz"
 	"github.com/openziti/storage/ast"
@@ -545,12 +546,16 @@ func (*BaseStore[E]) IteratorMatchingAnyOf(readIndex SetReadIndex, values []stri
 func (store *BaseStore[E]) CheckIntegrity(ctx MutateContext, fix bool, errorSink func(err error, fixed bool)) error {
 	for _, linkCollection := range store.links {
 		if err := linkCollection.CheckIntegrity(ctx, fix, errorSink); err != nil {
+			pfxlog.Logger().WithError(err).Infof("error checking link collection %s.%s -> %s.%s",
+				linkCollection.GetFieldSymbol().GetStore().GetEntityType(), linkCollection.GetFieldSymbol().GetName(),
+				linkCollection.GetLinkedSymbol().GetStore().GetEntityType(), linkCollection.GetLinkedSymbol().GetName())
 			return err
 		}
 	}
 	for _, constraint := range store.Indexer.constraints {
 		if err := constraint.CheckIntegrity(ctx, fix, errorSink); err != nil {
-			return err
+			pfxlog.Logger().WithError(err).Infof("error checking link constraint: %s", constraint.Label())
+			return errors.Wrapf(err, "error checking constraint: %s", constraint.Label())
 		}
 	}
 	return nil
diff --git a/boltz/system_entity_constraint.go b/boltz/system_entity_constraint.go
index 2dd8e7b..c0ecadf 100644
--- a/boltz/system_entity_constraint.go
+++ b/boltz/system_entity_constraint.go
@@ -1,6 +1,7 @@
 package boltz
 
 import (
+	"fmt"
 	"github.com/openziti/foundation/v2/errorz"
 	"github.com/pkg/errors"
 	"go.etcd.io/bbolt"
@@ -17,6 +18,11 @@ type systemEntityConstraint struct {
 	systemFlagSymbol EntitySymbol
 }
 
+func (index *systemEntityConstraint) Label() string {
+	return fmt.Sprintf("system entity constraint %s.%s",
+		index.systemFlagSymbol.GetStore().GetEntityType(), index.systemFlagSymbol.GetName())
+}
+
 func (self *systemEntityConstraint) checkOperation(operation string, ctx *IndexingContext) error {
 	t, val := self.systemFlagSymbol.Eval(ctx.Tx(), ctx.RowId)
 	isSystem := FieldToBool(t, val)
diff --git a/version b/version
index 3b04cfb..be58634 100644
--- a/version
+++ b/version
@@ -1 +1 @@
-0.2
+0.3