When working with a linked custom transformer, I often have to temporarily embed it to properly debug it. Then I have to export it to make it linked again. However, when I do that, any version history on the transformer is lost, as the versions start over at 1. This will, of course, break any other workspaces using the linked transformer that have not yet ready to upgrade to the new version.
When exporting, there needs to be an option to add a new version to the .fmx, rather than merely overwriting it.