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I'm looking for a GUI application for Windows or Linux which can modify MP4 boxes.

I don't want to edit the video, but I want to edit the fields in the boxes (I also do not want to insert or remove or reorder boxes).

Is there anything for this purpose or I will have to do it with a HEX-Editor?

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ExifTool is the goto tool for editing metadata of Images & Video files. It is a command line utility but there is also a GUI for Windows (or several) available there is also pyExifToolGUI which is cross platform.

Note that some metadata should not be tampered with, (as it can result in an unusable file), and ExifTool & the GUI honor the read-only flags. Attempting to edit with a hex editor is very likely to result in unusable files.

ExifToolGUI

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