diff --git a/pkg/db/topology.go b/pkg/db/topology.go
index 4c215cded..e201b152b 100644
--- a/pkg/db/topology.go
+++ b/pkg/db/topology.go
@@ -27,7 +27,7 @@ func PersistTopology(t *v1.Topology) (bool, error) {
 		return changed, err
 	}
 	tx := Gorm.Table("topologies").Clauses(clause.OnConflict{
-		Columns:   []clause.Column{{Name: "name"}, {Name: "namespace"}},
+		Columns:   []clause.Column{{Name: "agent_id"}, {Name: "name"}, {Name: "namespace"}},
 		UpdateAll: true,
 	}).Create(model)
 	if tx.Error != nil {
@@ -212,11 +212,14 @@ func GetChildRelationshipsForParentComponent(componentID uuid.UUID) ([]pkg.Compo
 }
 
 func PersistComponentRelationships(relationships []*pkg.ComponentRelationship) error {
-	tx := Gorm.Clauses(clause.OnConflict{
+	if len(relationships) == 0 {
+		return nil
+	}
+
+	return Gorm.Clauses(clause.OnConflict{
 		Columns:   []clause.Column{{Name: "component_id"}, {Name: "relationship_id"}, {Name: "selector_id"}},
 		UpdateAll: true,
-	}).Create(relationships)
-	return tx.Error
+	}).Create(relationships).Error
 }
 
 func GetCheckRelationshipsForComponent(componentID uuid.UUID) ([]pkg.CheckComponentRelationship, error) {
diff --git a/pkg/jobs/canary/canary_jobs.go b/pkg/jobs/canary/canary_jobs.go
index 5dc1b4e4b..f089f433a 100644
--- a/pkg/jobs/canary/canary_jobs.go
+++ b/pkg/jobs/canary/canary_jobs.go
@@ -256,6 +256,14 @@ func findCronEntry(id string) *cron.Entry {
 	return nil
 }
 
+func getAllCanaryIDsInCron() []string {
+	var ids []string
+	for _, entry := range CanaryScheduler.Entries() {
+		ids = append(ids, entry.Job.(CanaryJob).DBCanary.ID.String())
+	}
+	return ids
+}
+
 func ScanCanaryConfigs() {
 	logger.Infof("Syncing canary specs: %v", CanaryConfigFiles)
 	for _, configfile := range CanaryConfigFiles {
@@ -342,10 +350,13 @@ func SyncCanaryJobs() {
 		return
 	}
 
+	existingIDsInCron := getAllCanaryIDsInCron()
+	var idsInNewFetch []string
 	for _, c := range canaries {
 		jobHistory := models.NewJobHistory("CanarySync", "canary", c.ID.String()).Start()
 		_ = db.PersistJobHistory(jobHistory)
 
+		idsInNewFetch = append(idsInNewFetch, c.ID.String())
 		if err := SyncCanaryJob(c); err != nil {
 			logger.Errorf("Error syncing canary[%s]: %v", c.ID, err.Error())
 			_ = db.PersistJobHistory(jobHistory.AddError(err.Error()).End())
@@ -355,6 +366,11 @@ func SyncCanaryJobs() {
 		_ = db.PersistJobHistory(jobHistory.End())
 	}
 
+	idsToRemoveFromCron := utils.SetDifference(existingIDsInCron, idsInNewFetch)
+	for _, id := range idsToRemoveFromCron {
+		DeleteCanaryJob(id)
+	}
+
 	logger.Infof("Synced canary jobs %d", len(CanaryScheduler.Entries()))
 }