This issue is specific to Windows thanks its file system locking mechanism.
SceneBuilder may not be the sole use case but fact is that if you define two FX custom components, C1 made of pure Java code, and C2 defines thanks an FXML description then:
- you can import several times in a row C1
- the second time you import C2 you get a stack referencing the FXMLLoader

All the details are in DTL-6664 (stack, use case).

The analysis on SceneBuilder's side is that the FXMLLoader may held some references that prevent from reloading the exact same layout a second time.
To be honest we found what looked to be a good potential root cause in FXMLLoader's code a few months ago, didn't take note of it and didn't find it again while looking at it a few weeks ago, too bad.