And what about configuration files?

The configuration files of both platforms are committed under version control and I noticed they are ignored by the other platform. Eclipse shows an alert in the problems list, and the internal file used by NetBeans for automatic updating of ANT tasks is also marked as problem, but it has no impact on the development environment and the project normally compiles, runs and executes tests in both IDEs.

What is the big deal on using two IDEs in a same project?

In commercial projects, probably the best strategy is to bet in a unique platform and find a way to extract the best that IDE can give you, eventually including some platform specific tricks in your configuration to enhance your productivity. But technology is not static and sometimes it is nice to keep an open mind about what is going on in the open source community. I will not promote here another tiring comparison of IDE flame, we have enough of that in every Java mailing list, but I'd rather to post some positive thoughts from my personal experience:

NetBeans offers automatic updating of ANT tasks if you change artifacts and/or structure of your project. For example, if you include a new folder, NetBeans add its reference in your ANT tasks definition. The Sun IDE also offers an impressive i18n support with features to refactor old projects in order to verify missed constants.

On the other side, Eclipse is still the most comfortable Java editor available, fast and reliable.

Both IDEs offer a very good Subversion support and the most common development features without great differences - despite personal opinions, of course ;)

That's it for now, I am very happy with the recent advances of NetBeans IDE and I am for a long time fan of Eclipse, so what I suggest you to do is to try both IDEs and find out what best fits your project requirements. Afterwards, the best comparison available continues to be your own experience.