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Please refer to http://www.jar2exe.com/solutions/safety

I'm so sorry to hear that your encrypted program is hacked. For professional hackers, we are difficult to get it 100% safe, even for Windows or iOS, so what we can do is to let is more and more difficult to hack.

Jar2Exe does 2 things to protect java program (1) confusing the filename within jar file, (2) encrypt jar file.

Besides the protection of Jar2Exe, there are some other advices on doing more steps to protect java program: http://www.jar2exe.com/solutions/safety , that is to do an (3) abfuscation and (4) exe file encryption.