I have now done several tests in order to find out whether the bug you describe is caused by WinUAE or by the host operating system (Windows 8.x, 10).
It is not related to MS-Windows and the used file system (NTFS, FATxxx) - here all tests, regardless if WinUAE was fired up with administrative privileges or not, did not cause any issues (under AmigaOS3.x).
My best guess is that the issue is solely related to AmigaOS4.x, as I can't imagine that QEMU is the cause and no one ever spotted this strange behaviour before.
It would be interesting to know if other Linux tools that store binary data in big-endian format also suffer from this.
Kind regards.