I don’t buy this. Worst case scenario, the microscope talks to the PC using a proprietary hardware interface (say, an ISA card). It would cost far less than millions to hire a competent electronics engineer to reverse engineer the ISA card and the driver that talks to the ISA card, and fabricate a modern interface. Best case scenario, the microscope talks to the PC via a standard interface, and would be even cheaper to reverse, since you’d just need to worry about the software layer.
On the other hand, it would truly cost millions when the aforementioned ancient interface inevitably breaks and becomes impossible to reverse engineer, necessitating purchase of a brand new microscope.
>what they had apparently worked great
This is the real reason: because the scope works fine right now, nobody thought it prudent to invest the tens of thousands it would take to future-proof it. Exactly like companies that prioritize short-term profits over long-term success.