diff --git a/acceptance/bundle/config-remote-sync/config_edits/output.txt b/acceptance/bundle/config-remote-sync/config_edits/output.txt
index ff88716b3c..2a59c6f563 100644
--- a/acceptance/bundle/config-remote-sync/config_edits/output.txt
+++ b/acceptance/bundle/config-remote-sync/config_edits/output.txt
@@ -26,6 +26,7 @@ Resource: resources.jobs.my_job
   email_notifications.on_failure[0]: replace
   max_concurrent_runs: replace
   tags['env']: remove
+  timeout_seconds: remove
 
 
 
@@ -41,15 +42,16 @@ Resource: resources.jobs.my_job
 +              - remote-failure@example.com
            parameters:
              - name: catalog
-@@ -35,7 +35,6 @@
+@@ -35,8 +35,6 @@
                unit: DAYS
            tags:
 -            env: config-production
              team: data-team
 -          max_concurrent_runs: 3
+-          timeout_seconds: 3600
 +          max_concurrent_runs: 5
-           timeout_seconds: 3600
            environments:
+             - environment_key: default
 
 >>> [CLI] bundle destroy --auto-approve
 The following resources will be deleted:
diff --git a/bundle/configsync/defaults.go b/bundle/configsync/defaults.go
index 9b0157bf03..166a6bb38f 100644
--- a/bundle/configsync/defaults.go
+++ b/bundle/configsync/defaults.go
@@ -97,12 +97,20 @@ var serverSideDefaults = map[string]any{
 	"resources.pipelines.*.continuous": false,
 }
 
-func shouldSkipField(path string, value any) bool {
+// shouldSkipField checks if a field should be skipped in change detection.
+// When hasConfigValue is true (field is set in config or saved state), only
+// "always skip" fields are skipped. Backend defaults are only skipped when the
+// field is not in config/state, matching the behavior of shouldSkipBackendDefault
+// in the direct deployment engine.
+func shouldSkipField(path string, value any, hasConfigValue bool) bool {
 	for pattern, expected := range serverSideDefaults {
 		if matchPattern(pattern, path) {
 			if _, ok := expected.(skipAlways); ok {
 				return true
 			}
+			if hasConfigValue {
+				return false
+			}
 			if _, ok := expected.(skipIfZeroOrNil); ok {
 				return value == nil || value == int64(0)
 			}
diff --git a/bundle/configsync/diff.go b/bundle/configsync/diff.go
index 0d8bddc2e9..e483a3f943 100644
--- a/bundle/configsync/diff.go
+++ b/bundle/configsync/diff.go
@@ -70,7 +70,7 @@ func filterEntityDefaults(basePath string, value any) any {
 	for key, val := range m {
 		fieldPath := basePath + "." + key
 
-		if shouldSkipField(fieldPath, val) {
+		if shouldSkipField(fieldPath, val, false) {
 			continue
 		}
 
@@ -91,7 +91,7 @@ func convertChangeDesc(path string, cd *deployplan.ChangeDesc) (*ConfigChangeDes
 		return nil, fmt.Errorf("failed to normalize remote value: %w", err)
 	}
 
-	if shouldSkipField(path, normalizedValue) {
+	if shouldSkipField(path, normalizedValue, hasConfigValue) {
 		return &ConfigChangeDesc{
 			Operation: OperationSkip,
 		}, nil