If you can see the individual names also listed in the 'Structure View' panel, then your file should be recoverable.
From your description it sounds as if maybe some part of the graph got very large coordinate values. When you click on the '1:1' magnifying glass tool (in the tool bar), you should be able to see your diagram at 100% size. Maybe there is one element very far away from all others.
If this doesn't help and/or you want us to take a look at your file, please see http://yed.yworks.com/support/qa/1734, which explains how to upload a file to the yEd Q&A. (Since this question was posted anonymously, uploading to it is unfortunately not possible, i.e. you will have to upload in the context of a new question.)