At the very least, being able to read the source code gives you a Hell of a head start on writing a new driver for an appropriate OS (and by that I mean Linux, obviously). Saves a whole reverse-engineering step.
I’m not saying creating an entire project to adapt the controller and software stack to modern systems would be cheap or easy, but it’s possible – and more to the point, seemingly less expensive than buying the new microscope for “hundreds of thousands of €” (especially in the long run, since the company is likely to pull the same shit over and over again), even if you’ve got to pay a gaggle of comp-e grad students to put it together for you.