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I'm not aware of any way to change 50 file names simultaneously. You'll need to do them one a time. 50 should take no longer than a couple of minutes.
You can also do the "slow" 2 click routine on the file name. Click once to select, click one more time for editing. Change name, click outside the file name and EWD will save and update all references.
Hopefully you are setting up a 301 permanent redirect from the old files to the new files before making these changes?