Found yet another bug:
When exporting to Godot, I had to change the export path, because it’s different in the different machines we use.
The export will report success even when the path does not exists, and no files are generated.
Furthermore, if you update the export path without restarting, the export will work (as expected?), but will write absolute paths in the Resource files, not relatives.
Restarting will fix the issue, and Resources will be exported properly, with relative paths.