diff --git a/bundle/config/mutator/apply_source_linked_deployment_preset.go b/bundle/config/mutator/apply_source_linked_deployment_preset.go
index 839648301..570ca72cf 100644
--- a/bundle/config/mutator/apply_source_linked_deployment_preset.go
+++ b/bundle/config/mutator/apply_source_linked_deployment_preset.go
@@ -72,17 +72,18 @@ func (m *applySourceLinkedDeploymentPreset) Apply(ctx context.Context, b *bundle
 		return diags
 	}
 
+	// This mutator runs before workspace paths are defaulted so it's safe to check for the user-defined value
 	if b.Config.Workspace.FilePath != "" && config.IsExplicitlyEnabled(b.Config.Presets.SourceLinkedDeployment) {
-		path := dyn.NewPath(dyn.Key("targets"), dyn.Key(target), dyn.Key("workspace"), dyn.Key("file_path"))
-
+		path := dyn.NewPath(dyn.Key("workspace"), dyn.Key("file_path"))
 		diags = diags.Append(
 			diag.Diagnostic{
 				Severity: diag.Warning,
 				Summary:  "workspace.file_path setting will be ignored in source-linked deployment mode",
+				Detail:   "In source-linked deployment files are not copied to the destination and resources use source files instead",
 				Paths: []dyn.Path{
-					path[2:],
+					path,
 				},
-				Locations: b.Config.GetLocations(path[2:].String()),
+				Locations: b.Config.GetLocations(path.String()),
 			},
 		)
 	}
diff --git a/bundle/deploy/metadata/compute.go b/bundle/deploy/metadata/compute.go
index b47baa6b2..633d97081 100644
--- a/bundle/deploy/metadata/compute.go
+++ b/bundle/deploy/metadata/compute.go
@@ -54,6 +54,7 @@ func (m *compute) Apply(_ context.Context, b *bundle.Bundle) diag.Diagnostics {
 
 	// Set file upload destination of the bundle in metadata
 	b.Metadata.Config.Workspace.FilePath = b.Config.Workspace.FilePath
+	// In source-linked deployment files are not copied and resources use source files, therefore we use sync path as file path in metadata
 	if config.IsExplicitlyEnabled(b.Config.Presets.SourceLinkedDeployment) {
 		b.Metadata.Config.Workspace.FilePath = b.SyncRootPath
 	}