First, try to reduce your problem: obfuscate single file, then - small jar, and then - war file.
Second, post here more detailed info: how your file looks, what is your obfuscation config, what is your proguard version, etc.
Maybe then someone will be able to help.
But first - look at first point and try to solve your problem by reduction. It works in 99% cases.
subject: Proguard output file does not include my java code - Help required