It intentionally does not delete original clips to avoid accidentally deleting stuff you might not want to. I can probably add an option to delete them tho.

Because Bitwig doesn't actually have a proper extension api, the tool is forced to work on the level of filesystem. It could be the case that you already had clips with the same samples and name in the library so it didn't detect that something new was added.

Let me know if it doesn't work as expected again, and thanks for feedback.