Here is how the new update window will look like (in main themaCreator program):
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updateWindow.PNG [ 57.67 KiB | Viewed 423 times ]
You can open the themaUpdater.exe at any time as well (but not really needed), it won't damage anything, you would just see this window:
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Updater.PNG [ 52.45 KiB | Viewed 423 times ]
Screenshots from themaPoster, but they are exactly the same in all programs.
It is fairly smart to handle most cases (at least I tried to think of all rare cases which could happen).
It will automatically close the main program if it's running, or if it can't it will offer a button to "Force close".