BW> I noticed that when I removed a file (MyGUI v1.0.2.26.zip) from disk and
 BW> ran ./mutil -run PackFileBases afterwards, mutil did not flag the
 BW> missing file as offline, but merely as having a 0-byte file size.
 BW> 
 BW> Do you know what could be causing this?

This is a bug that should be fixed in the next A48 build. :)

... When cheese gets its picture taken, what does it say?

--- Mystic BBS v1.12 A48 2022/01/28 (Windows/64)