Wouldn't a virus self-replicate? And perhaps be able to add/delete cogs from one's difference engine? Perhaps you could make one that can replicate, with a sibling in some partial stage of completion...
Such a mechanism could also punch new holes or plaster over older holes in punchcards found in load hoppers of difference engines. That would be a more frightening thought, as scanning the holes of punchcards as they pass through the reader is not an easy process.
Hmmm... viruses often replicate through the mail. I can foresee a version that can travel by pneumatic tube. Drat! Since my engine is connected to the Ætherweb, I needs must build a 'firewall'. I'd best put in an order for more coal.
"Excuse me.. I say.. where did my pocket watch go?"
Perhaps mesh filters would be advisable in my own pneumotube port...
*runs to the junk shop*