Seems to me that the 'cheat' (working the letter of the law to an unintended consequence is more accurate, but hardly easy to say) was there to try and protect the lifetime of the emissions reduction equipment. VW is hardly interested in committing even more costs to make such equipment last 100k miles being 'on' ALL the freakin' time, when you can make it much cheaper if you can figure out how to make it last only part of the time. And as we all know, lower costs mean more profit, and the shareholders like that part of the game more than anything else.
Having said that, I seriously doubt there would be damage to the actual engine part of this whole thing due to programming and/or emissions equipment changes.
Except (and what follows is my conjecture, since I am not privy to any of the fix details): when a regen cycle is run, IIRC, the extra heat is supplied by enriching the exhaust with diesel injected during the exhaust cycle. That extra fuel can stick to the cylinder walls and cause trouble, that trouble being minimized when the engine is hot due to the volatility of diesel. They're counting on the extra fuel vaporizing instead of fuel droplets hitting the cylinder walls. Which of course, leads to why VW doesn't like biodiesel or blends thereof in any of their diesels, and especially the DPF equipped CR engines. Bio-D doesn't vaporize nearly as well as dino-diesel.
This, of course, leads back to the 'cleaner' solution: that of just adding an extra injector outside of the engine in the exhaust stream somewhere. VW didn't want to do that, however, since it costs more. Sigh...
The upshot is, back to the original question, is that the more heavily used fuel enrichment of the exhaust will probably be used more in the fixes, so the possible problem of unburned or partially burned fuel making it into the crankcase and diluting the oil might be a problem.
Keep an eye on the engine oil.
Cheers,
PH
