Tested on linux, seems to work fine.
Preliminary tests suggest that hyperlinks/footnotes work fine.
I notice that the temp folder (you use one single folder for successive EbookScramble actions) is not being cleaned up. One of the books I tested was a giant comic with lots of sizeable pictures!

And the original file appeared in three places...
(And it does get cleaned up when calibre quit. Maybe that's why it took so long to quit.... Maybe it is a limit of calibre's tempfiles handling.)
But cleanup aside, it seems to be working.
...
Haven't tried any SVG images, I'll let you know
if I find any.