I use QQ routinely without seeing that happen.
The default epub update mode shouldn't truncate stories, that suggests you're using Overwrite instead.
Unlike for most sites supported by FFF, giving a 'chapter' or individual post URL for Xenforo sites (QQ/SB/SV/etc) makes a story from that one post alone, or from the posts linked in it.
So if you using Overwrite *and* individual post URLs instead of the thread URL, that might explain it.