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User files do not get overwritten in updates. (Unless you're doing something really strange like adding them to files added by the community pack or some other downloaded user content.)
Character...Configure Hero will bring up the settings list for a character. ctrl-k is the keyboard shortcut for this command.
Make sure that if you are creating new files in the editor, they must be saved in the default directory - nowhere else, and not within sub-folders of that directory. Tools...Explore Folders...Game System Data Folder will take you to the correct folder. This is the usual reason for the symptoms you're describing - the "Test Now!" operation works regardless of where the file is saved, but when you next start the program, if the files aren't where they're supposed to be, Hero Lab won't include them.
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