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Why not save the files you want to keep BEFORE you delete them using the Save to Disk feature? You can do that in bulk; just mark every file, select "show marked files", select them all and save to disk. You can also do that with individual files before any merging operations.
Deciding to keep a file after you've deleted them seems a very inefficient way of saving something.
And of course keeping a backup copy of your library is always a good idea.
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