How to handle the different dialects of regular expressions (java vs. xsd)?

Although it may not be the best solution in the world, you could consider using the Sax parser. I have used it for over 3 years now, however I have not done much regex validation with it, so I cannot speak to it's robustness related to that.

Other than that, I think Kaleb is probably correct on the preprocessing side (which is anything but ideal) - you might be able to use a regex for any of the incoming regex'es to do a replace.... although that has quite the code smell about it.

Edit: An additional thought that just came to me. If the regex does not need to be in the xsd - i.e. it is there simply because that was "easiest" in the past - you could do the regex validation outside of the xsd. But, if other systems use the xsd, that is likely not the correct solution, and you can forget I said anything.