diff --git a/seed/target.go b/seed/target.go
index 9f665ee8d..9c0ce4e14 100644
--- a/seed/target.go
+++ b/seed/target.go
@@ -4,6 +4,7 @@ import (
 	"container/list"
 	"errors"
 	"fmt"
+	"slices"
 
 	liberr "github.com/jortel/go-utils/error"
 	"github.com/konveyor/tackle2-hub/model"
@@ -97,6 +98,11 @@ func (r *Target) Apply(db *gorm.DB) (err error) {
 		seedIds = append(seedIds, target.ID)
 	}
 
+	err = r.deleteUnwanted(db)
+	if err != nil {
+		return
+	}
+
 	err = r.reorder(db, seedIds)
 	if err != nil {
 		return
@@ -104,6 +110,35 @@ func (r *Target) Apply(db *gorm.DB) (err error) {
 	return
 }
 
+// deleteUnwanted deletes targets with a UUID not found
+// in the set of seeded targets.
+func (r *Target) deleteUnwanted(db *gorm.DB) (err error) {
+	var found []*model.Target
+	err = db.Find(&found).Error
+	if err != nil {
+		err = liberr.Wrap(err)
+		return
+	}
+	wanted := make(map[string]byte)
+	for _, t := range r.targets {
+		wanted[t.UUID] = 0
+	}
+	for _, target := range found {
+		if target.UUID == nil {
+			continue
+		}
+		if _, found := wanted[*target.UUID]; found {
+			continue
+		}
+		err = db.Delete(target).Error
+		if err != nil {
+			err = liberr.Wrap(err)
+			return
+		}
+	}
+	return
+}
+
 // reorder updates the value of the ui.target.order setting
 // to add any missing target ids. (namely, newly added targets.)
 func (r *Target) reorder(db *gorm.DB, seedIds []uint) (err error) {
@@ -126,7 +161,7 @@ func (r *Target) reorder(db *gorm.DB, seedIds []uint) (err error) {
 	}
 	userOrder := []uint{}
 	_ = s.As(&userOrder)
-	s.Value = merge(userOrder, seedIds, targetIds)
+	s.Value = r.merge(userOrder, seedIds, targetIds)
 
 	result = db.Where("key", UITargetOrder).Updates(s)
 	if result.Error != nil {
@@ -142,11 +177,13 @@ func (r *Target) reorder(db *gorm.DB, seedIds []uint) (err error) {
 //	  userOrder: slice of target IDs in the user's desired order
 //	  seedOrder: slice of target IDs in seedfile order
 //	  ids: slice of ids of all the targets in the DB
-func merge(userOrder []uint, seedOrder []uint, ids []uint) (mergedOrder []uint) {
+func (r *Target) merge(userOrder []uint, seedOrder []uint, ids []uint) (mergedOrder []uint) {
 	ll := list.New()
 	known := make(map[uint]*list.Element)
 	for _, id := range userOrder {
-		known[id] = ll.PushBack(id)
+		if slices.Contains(ids, id) {
+			known[id] = ll.PushBack(id)
+		}
 	}
 	for i, id := range seedOrder {
 		if _, found := known[id]; found {
diff --git a/seed/target_test.go b/seed/target_test.go
index 0505b55d5..d46a8bdc7 100644
--- a/seed/target_test.go
+++ b/seed/target_test.go
@@ -9,6 +9,8 @@ import (
 func TestMerge(t *testing.T) {
 	g := gomega.NewWithT(t)
 
+	seeder := Target{}
+
 	// the seed contains 10 targets in a given order, 3 of which are new
 	seedOrder := []uint{1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
 	// the user has set up a custom order for the 7 targets that already exist in the db
@@ -20,6 +22,6 @@ func TestMerge(t *testing.T) {
 	// that had previously been dropped on the floor being added to the end of the ordering.
 	expectedOrder := []uint{6, 7, 8, 9, 10, 5, 4, 1, 3, 2, 11, 12, 13}
 
-	mergedOrder := merge(userOrder, seedOrder, allIds)
+	mergedOrder := seeder.merge(userOrder, seedOrder, allIds)
 	g.Expect(mergedOrder).To(gomega.Equal(expectedOrder))
 }