In an operating system, when a file is opened and changing, other programs cannot see changes, or cannot even access it.
I've successfully reproduced this, with 10 files, only 4 in archive, and their contents are all \x00.
Maybe it's the file just got "immutable" when writing. (I'm not a low-level os expert)
So the solution is, keep the files closed when trying to access (archive) them.
You can try to close your file-writing applications, locally or remotely.
With HFS, you can do with macros. Be sure to keep secure.
P.S. What I've tried is following python code:
files = []
for i in range(10):
files.append(open(str(i) + '.txt', 'w', encoding='utf-8'))
while True:
for i in files:
i.seek(0)
i.write('1')
It infinitely writes the file on the first byte (char) until Ctrl+C.