What works for me is to double-click the server instance in Eclipse. It opens up the details. Near the right bottom corner, there is an option for "Debug". Expand it and uncheck the "Resolve sources when connecting".
This stops Eclipse from comparing your Eclipse code with the code running inside the server. This isn't an ideal answer. Ideally, we want to sync the Eclipse code with the server code, otherwise debugging has no meaning -- assume you're off by even one line of code when debugging.
I'm answering your specific question. For a broader answer on this, please see:
Eclipse java debugging: source not found