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I would suggest you create a new MyEclipse web project and then transfer the code from the Eclipse to the MyEclipse project. That is a sure shot way of getting the project to work.
1. If the project is already checked out, you can just check the changes back in from the Team menu by right-clicking on the project.
2. If the project is just a local project, you can import it into the SVN repository by right-clicking, going to Team > Share, and then walking through the import process.