I thought about this some more since someone else was just affected. I am thinking there could be two reasons outside of Shotcut since Shotcut now validates the file saved as valid XML (no NUL).
- Some security product zeroes a file after a deletion
- Something going wrong with disk write-back caching
I found this post from a NTFS developer supporting my second guess:
Some other reply gives a corrupt disk as a reason. More ideas and people facing this same problem while not using Shotcut can be found in a web search on “windows save nul”.