yEd is wonderful for editing graphs. What I find the most bothersome is the export facility. Perhaps the following would save us all repetitive work:
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Split "Export..." into "Export" and "Export As..."
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The "Export As..." choice permits multiple exports at once
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The "Export" choice repeates prior export; it looks for files with the typical extensions to learn export formats used before (and may validate that by looking into metadata in that format if protection from overwriting is a concern); it may additionally or alternatively use information from an explicit "Export As..." in the same session
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The format popups are shown with "Export As..." but not for "Export"
What this enables is expedited export after having made a change. It is perfectly possible with yEd to support a plethora of formats, but supporting multiple at the same time causes quite a bit of manual work.