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This is probably because a build is triggered, which causes the classes folder to be cleared. This is the normal way Eclipse operates. Don’t you have the source code for your beans in the java source folder of the project? How did you get them there to begin with?
I compile those java files in other java package, then I drag the whole folder into the jsp project classes folder. When I add some external these java file needed, it cleared everything in the classes foler from class to .java files. Is this clear the point or correct way to do it?
Pay particular attention to the 4th post (by Support) that explains how to set the output location of your other project to be your web project’s classes directory. That should do what you want.