tahts hard to answer, as i don't know the cobain backup software, but i don't think it would be possible as HFS save its files and settings to 3 locations
hfs > expert mode > save options
either the ini file, which you manual must select through the hfs gui
or the registy,which you manual must select through the hfs gui
and the main one that is normally selected, save VFS a local file....
My understanding of how your backup program / if it works like this would be:
hfs running, cobain backup deos a file copy - zip archive at that point in time
--when HFS is running with out that saved file, then there is no backup as HFS upon launch may hfs the website files but not its structure nor stuff inside...
so there will need to be some tweaking to the template to auto save a vfs/registy/ini
i did a run about with it saving on close with a script that would close it, hfs upon closing would save the vfs, and start hfs again
i assume when it is offline like that that you could impose a file copy backup...
other wise a more advance user would be need here