I don't think the outlook is as bleak as those here seem to believe. Roughly 20% of the 501 fleet has been converted to the FJ44 engines since 2002. These airplanes are flown regularly, so someone obviously sees some utility in owning them.
The converted 501's fill a niche between the VLJ's and the CJ2. The speed and range exceed that of a CJ1 and the Mustang. Until the price of used CJ2's reaches around $2 million, there's nothing else that can touch the converted 501's, as far as operating costs and performance.
There's also a contingent of older owner pilots, who don't want to learn glass, and had just as well stick with their 501's with the retrofitted engines.
I don't know all the euro airspace acronyms spoken of, but I do know there are endless avionics upgrades available that make the 501 compatible with any changes forthcoming in US airspace. Whether that applies internationally or not, I don't know.
As far as the converted airplanes being black sheep, there is what's known as a STC, as I'm sure all posters are aware of. It isn't like some guy's secretly mounting these engines in a hangar somewhere. There are appropriate AFM supplements issued by the STC holder. There's nothing radical going on here, that is going to alter the airplane's safety.
So Cessna won't touch them, but it shouldn't be too hard to find someone to work on an old Citation.
Upgrading engines on existing airframes isn't anything new.
Whether 35 years old, or 5 years old, the pedigree of the individual airplane is more important than age. And most of the 501's on the market have <10,000 hours on them. Most often flown 200 hours a year or so, by private owners.