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I don't know, for as far as I know the files are deleted permanently. Or you have to use a program to recover files from your hard-disk. If you have a lot of space left on your hard-disk there is a fairly large chance that you can recover some savegame files. No guarantees though.
I don't know how to do any of this, I'm rubbish with computers, in my new AAR I'm making a backup after every chapter to avoid anything ever again.
Just make sure when you use the clean-up program that you check that it doesn't delete the .eu3 files. Don't just copy it to somewhere else on your computer, but on en external device.
That should to the trick, although not losing your save games at all would off course be better 
Next time you clean your computer with the cleaner, make sure you uncheck the .eu3 files.
Next time you clean your computer with the cleaner, make sure you uncheck the .eu3 files.