I don’t see how this could happen on the HTML-Kit Tools side of things. I say HTML-Kit Tools because the post was categorized under it.
I do remember HTML-Kit 292 (before Tools) having an option to make a duplicate under *.bak for backup purposes. That option is under “Edit > Preferences > Save > Backup when saving”. Even that shouldn’t break links because the original file is never removed.
In either case, I’d have to assume this is happening outside of HTML-Kit.