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That may depend on the particular tool you used to compile your executable. If you happened to use Pyinstaller, you can use the --onefile prefix when compiling on the command line.

unfortunatly --onefile does not work according to the customtkinter documentation. 

https://github.com/TomSchimansky/CustomTkinter/wiki/Packaging#windows-pyinstalle...

Hm, well --onedir appears to work. If you can pack all the dependencies into a single directory, then you can pack that into a zip file for distribution as well, then update the files in the zip as needed when updating.