This does not happen if Xindice is restarted after collection creation, because then on deletion the physical files are correctly deleted. This makes me believing Xindice incorrectly holds a handle after collection creation. But this does not happen on Linux.
Thanks for the head's up. All of my development is done on various UNIXes, so I wouldn't have found this on my own. There's a Windows box at the office that I can try to test it out on.
-- Tom Bradford - http://www.tbradford.org Developer - Apache Xindice (Native XML Database) Creator - Project Labrador (Web Services Framework)