Updating a theme

The name change by itself will not cause any problems, as long as the file header info is unique between them. https://codex.wordpress.org/File_Header

Why not use the version meta on the theme and retain the same name and directory structure for the theme?

You could also place the files in a proper version control system. Host the theme somewhere like Github or Beanstalk and use the tools that exist to manage version control.

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