diff --git a/bundle/config/resources.go b/bundle/config/resources.go
index 0affb6ef..2886e357 100644
--- a/bundle/config/resources.go
+++ b/bundle/config/resources.go
@@ -41,6 +41,9 @@ type ConfigResource interface {
 
 	// InitializeURL initializes the URL field of the resource.
 	InitializeURL(baseURL url.URL)
+
+	// IsNil returns true if the resource is nil, for example, when it was removed from the bundle.
+	IsNil() bool
 }
 
 // ResourceGroup represents a group of resources of the same type.
@@ -57,6 +60,9 @@ func collectResourceMap[T ConfigResource](
 ) ResourceGroup {
 	resources := make(map[string]ConfigResource)
 	for key, resource := range input {
+		if resource.IsNil() {
+			continue
+		}
 		resources[key] = resource
 	}
 	return ResourceGroup{
diff --git a/bundle/config/resources/clusters.go b/bundle/config/resources/clusters.go
index eb0247c6..ba991e86 100644
--- a/bundle/config/resources/clusters.go
+++ b/bundle/config/resources/clusters.go
@@ -56,3 +56,7 @@ func (s *Cluster) GetName() string {
 func (s *Cluster) GetURL() string {
 	return s.URL
 }
+
+func (s *Cluster) IsNil() bool {
+	return s.ClusterSpec == nil
+}
diff --git a/bundle/config/resources/dashboard.go b/bundle/config/resources/dashboard.go
index 724b0339..5c58a2f2 100644
--- a/bundle/config/resources/dashboard.go
+++ b/bundle/config/resources/dashboard.go
@@ -79,3 +79,7 @@ func (r *Dashboard) GetName() string {
 func (r *Dashboard) GetURL() string {
 	return r.URL
 }
+
+func (r *Dashboard) IsNil() bool {
+	return r.Dashboard == nil
+}
diff --git a/bundle/config/resources/job.go b/bundle/config/resources/job.go
index 98db1ec5..0aa41b2e 100644
--- a/bundle/config/resources/job.go
+++ b/bundle/config/resources/job.go
@@ -63,3 +63,7 @@ func (j *Job) GetName() string {
 func (j *Job) GetURL() string {
 	return j.URL
 }
+
+func (j *Job) IsNil() bool {
+	return j.JobSettings == nil
+}
diff --git a/bundle/config/resources/mlflow_experiment.go b/bundle/config/resources/mlflow_experiment.go
index a5871468..5d179ec0 100644
--- a/bundle/config/resources/mlflow_experiment.go
+++ b/bundle/config/resources/mlflow_experiment.go
@@ -58,3 +58,7 @@ func (s *MlflowExperiment) GetName() string {
 func (s *MlflowExperiment) GetURL() string {
 	return s.URL
 }
+
+func (s *MlflowExperiment) IsNil() bool {
+	return s.Experiment == nil
+}
diff --git a/bundle/config/resources/mlflow_model.go b/bundle/config/resources/mlflow_model.go
index 9ead254d..72376f45 100644
--- a/bundle/config/resources/mlflow_model.go
+++ b/bundle/config/resources/mlflow_model.go
@@ -58,3 +58,7 @@ func (s *MlflowModel) GetName() string {
 func (s *MlflowModel) GetURL() string {
 	return s.URL
 }
+
+func (s *MlflowModel) IsNil() bool {
+	return s.Model == nil
+}
diff --git a/bundle/config/resources/model_serving_endpoint.go b/bundle/config/resources/model_serving_endpoint.go
index 7f3ae00c..a3c472b3 100644
--- a/bundle/config/resources/model_serving_endpoint.go
+++ b/bundle/config/resources/model_serving_endpoint.go
@@ -66,3 +66,7 @@ func (s *ModelServingEndpoint) GetName() string {
 func (s *ModelServingEndpoint) GetURL() string {
 	return s.URL
 }
+
+func (s *ModelServingEndpoint) IsNil() bool {
+	return s.CreateServingEndpoint == nil
+}
diff --git a/bundle/config/resources/pipeline.go b/bundle/config/resources/pipeline.go
index b3311d8e..eaa4c536 100644
--- a/bundle/config/resources/pipeline.go
+++ b/bundle/config/resources/pipeline.go
@@ -58,3 +58,7 @@ func (p *Pipeline) GetName() string {
 func (s *Pipeline) GetURL() string {
 	return s.URL
 }
+
+func (s *Pipeline) IsNil() bool {
+	return s.PipelineSpec == nil
+}
diff --git a/bundle/config/resources/quality_monitor.go b/bundle/config/resources/quality_monitor.go
index 30ec4f91..b1d7e08a 100644
--- a/bundle/config/resources/quality_monitor.go
+++ b/bundle/config/resources/quality_monitor.go
@@ -62,3 +62,7 @@ func (s *QualityMonitor) GetName() string {
 func (s *QualityMonitor) GetURL() string {
 	return s.URL
 }
+
+func (s *QualityMonitor) IsNil() bool {
+	return s.CreateMonitor == nil
+}
diff --git a/bundle/config/resources/registered_model.go b/bundle/config/resources/registered_model.go
index c44526d0..8513a79a 100644
--- a/bundle/config/resources/registered_model.go
+++ b/bundle/config/resources/registered_model.go
@@ -68,3 +68,7 @@ func (s *RegisteredModel) GetName() string {
 func (s *RegisteredModel) GetURL() string {
 	return s.URL
 }
+
+func (s *RegisteredModel) IsNil() bool {
+	return s.CreateRegisteredModelRequest == nil
+}
diff --git a/bundle/config/resources/schema.go b/bundle/config/resources/schema.go
index a9f905cf..8eadd7e4 100644
--- a/bundle/config/resources/schema.go
+++ b/bundle/config/resources/schema.go
@@ -56,3 +56,7 @@ func (s *Schema) UnmarshalJSON(b []byte) error {
 func (s Schema) MarshalJSON() ([]byte, error) {
 	return marshal.Marshal(s)
 }
+
+func (s *Schema) IsNil() bool {
+	return s.CreateSchema == nil
+}
diff --git a/bundle/render/render_text_output_test.go b/bundle/render/render_text_output_test.go
index cd9e7723..135d79da 100644
--- a/bundle/render/render_text_output_test.go
+++ b/bundle/render/render_text_output_test.go
@@ -519,6 +519,10 @@ func TestRenderSummary(t *testing.T) {
 						URL:         "https://url2",
 						JobSettings: &jobs.JobSettings{Name: "job2-name"},
 					},
+					"job3": {
+						ID:  "3",
+						URL: "https://url3", // This emulates deleted job
+					},
 				},
 				Pipelines: map[string]*resources.Pipeline{
 					"pipeline2": {
diff --git a/bundle/resources/completion_test.go b/bundle/resources/completion_test.go
index 2f7942aa..80412b6f 100644
--- a/bundle/resources/completion_test.go
+++ b/bundle/resources/completion_test.go
@@ -6,6 +6,8 @@ import (
 	"github.com/databricks/cli/bundle"
 	"github.com/databricks/cli/bundle/config"
 	"github.com/databricks/cli/bundle/config/resources"
+	"github.com/databricks/databricks-sdk-go/service/jobs"
+	"github.com/databricks/databricks-sdk-go/service/pipelines"
 	"github.com/stretchr/testify/assert"
 )
 
@@ -14,11 +16,17 @@ func TestCompletions_SkipDuplicates(t *testing.T) {
 		Config: config.Root{
 			Resources: config.Resources{
 				Jobs: map[string]*resources.Job{
-					"foo": {},
-					"bar": {},
+					"foo": {
+						JobSettings: &jobs.JobSettings{},
+					},
+					"bar": {
+						JobSettings: &jobs.JobSettings{},
+					},
 				},
 				Pipelines: map[string]*resources.Pipeline{
-					"foo": {},
+					"foo": {
+						PipelineSpec: &pipelines.PipelineSpec{},
+					},
 				},
 			},
 		},
@@ -36,10 +44,14 @@ func TestCompletions_Filter(t *testing.T) {
 		Config: config.Root{
 			Resources: config.Resources{
 				Jobs: map[string]*resources.Job{
-					"foo": {},
+					"foo": {
+						JobSettings: &jobs.JobSettings{},
+					},
 				},
 				Pipelines: map[string]*resources.Pipeline{
-					"bar": {},
+					"bar": {
+						PipelineSpec: &pipelines.PipelineSpec{},
+					},
 				},
 			},
 		},
diff --git a/bundle/resources/lookup_test.go b/bundle/resources/lookup_test.go
index b2eaafd1..0ea5af7a 100644
--- a/bundle/resources/lookup_test.go
+++ b/bundle/resources/lookup_test.go
@@ -7,6 +7,7 @@ import (
 	"github.com/databricks/cli/bundle/config"
 	"github.com/databricks/cli/bundle/config/resources"
 	"github.com/databricks/databricks-sdk-go/service/jobs"
+	"github.com/databricks/databricks-sdk-go/service/pipelines"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -28,8 +29,12 @@ func TestLookup_NotFound(t *testing.T) {
 		Config: config.Root{
 			Resources: config.Resources{
 				Jobs: map[string]*resources.Job{
-					"foo": {},
-					"bar": {},
+					"foo": {
+						JobSettings: &jobs.JobSettings{},
+					},
+					"bar": {
+						JobSettings: &jobs.JobSettings{},
+					},
 				},
 			},
 		},
@@ -45,10 +50,14 @@ func TestLookup_MultipleFound(t *testing.T) {
 		Config: config.Root{
 			Resources: config.Resources{
 				Jobs: map[string]*resources.Job{
-					"foo": {},
+					"foo": {
+						JobSettings: &jobs.JobSettings{},
+					},
 				},
 				Pipelines: map[string]*resources.Pipeline{
-					"foo": {},
+					"foo": {
+						PipelineSpec: &pipelines.PipelineSpec{},
+					},
 				},
 			},
 		},
@@ -92,10 +101,14 @@ func TestLookup_NominalWithFilters(t *testing.T) {
 		Config: config.Root{
 			Resources: config.Resources{
 				Jobs: map[string]*resources.Job{
-					"foo": {},
+					"foo": {
+						JobSettings: &jobs.JobSettings{},
+					},
 				},
 				Pipelines: map[string]*resources.Pipeline{
-					"bar": {},
+					"bar": {
+						PipelineSpec: &pipelines.PipelineSpec{},
+					},
 				},
 			},
 		},