This week's book giveaways are in the Refactoring and Agile forums. We're giving away four copies each of Re-engineering Legacy Software and Docker in Action and have the authors on-line! See this thread and this one for details.
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.