Create a new FXML layout, drop a Button on Content, save as say whatever.fxml
Use Preview menu entries to:
- set a background color
- set a style sheet
- set a resource bundle
File > Save
The FXML file content is (extract):

<?scenebuilder-background-color 0xbc66ffff?>
<?scenebuilder-preview-i18n-resource ../authoringtool/samples/HelloI18N/src/helloi18n/Bundle.properties?>
<?scenebuilder-stylesheet ../authoringtool/samples/IssueTrackingLite/src/issuetrackinglite/IssueTrackingLite.css?>

This is dramatically perfect.
Now close whatever.fxml, move it on disk to another directory and re-open it within SceneBuilder.
The expected behavior is to get two warnings saying that both the resource bundle and the stylesheet file cannot be loaded, their respective path being irrelevant.
Fact is the expected warnings come up. Lovely.

Now move the Button on Content to become able to take File > Save.
The problem is that in FXML file I now read:

<?scenebuilder-background-color 0xbc66ffff?>
<?scenebuilder-stylesheet ../authoringtool/samples/IssueTrackingLite/src/issuetrackinglite/IssueTrackingLite.css?>

==> the resource bundle line is gone while the stylesheet line has been kept: for both their respective path is wrong so one expects they're handled the same.
My take is that the stylesheet line should have been removed too because keeping it let the user think there's still a styling ON (Preview > Remove a Style Sheet > sub-menu is not empty).