Reload tells SBT to read the build files. If your ran the eclipse command in an already running SBT shell after you edited the build files before you ran reload, it would not "know about" the updated build file. And running reload after eclipse doesn't help eclipse.
So in short, after you edit the build file you need to either run sbt eclipse, run sbt and enter eclipse in the new SBT shell, or run reload in an existing SBT shell and then enter eclipse.
That will regenerate the eclipse files from sbt's state.
Getting eclipse to reload your eclipse configuration files depends on its settings.
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