Some version of Microsoft Windows OS have rather dangerous subsystem known as MP4 property sheet handler (“MF MPEG-4 Property Handler” to be exact). Programmatically, you would use API like SHGetPropertyStoreFromParsingName and use IPropertyStore from there to read (reading is OK) and update/write certain MP4 file properties like, for example, a comment or som other metadata.
The same API is used from property sheet UI if you decide to update metadata:
It looks like the implementation is damaging some media files. An attempt to update a file breaks it and overwrites vital part of MPEG-4 Part 14 file structure with the new metadata, rendering the file unplayable.
Long story short – prefer to not use the API at all to update the metadata, or make a backup copy.
In DirectShow MP4 multiplexer created back in time by Geraint Davies, in its fork I am still using somewhere, I created IMuxFilter::SetComment method exactly for this: to be able to set comment before the file is finalized, by injecting a respective box with metadata as a part of finalization, so that stock faulty Windows API is not used and the produced file is reliably safe.