Got you. However, how do you know about C and D. I think one would literally have to look at the basedir on the filesystem (provided this is even possible given the directory type)

Well I would not need to know about C or D. An option would say, blow everything in the index and we would delete all elements regardless of _hibrnate_class's presence or value.
If that option is off, then we would only delete A and B with the currently crafted deleted querues.