One thing to consider is that the employee might not have been a programmer in IT. The description of what he developed sounds like a custom process developed in MS Access or some other software used in the business side of the office.
It also sounds like a custom application developed in house of something that might be available in shrinkwrap or download form, but it's "missing a main component that is important to us because our place is unique with special needs that are not on the market."
Which is usually not true, but management often forgets the payroll cost and opportunity cost of having a worker develop something custom instead of paying for a developed commercial software product. Then the developer leaves and in a few years something breaks and nobody knows how to fix it.
This was my first thought, too.
I had something similar happen to me during an odd eddy in my career path. I was a college-trained professional programmer going back to the mainframe days. After the completion of a major multi-year IT project decades later, I was misplaced in the "business unit" supporting the business help desk staff. Out of place for my skillset, I took it upon myself to build an Access database and front-end GUI to support the support staff of 100 people to respond to and fix reported system issues.
After single-handedly building a prioritization system that got a dozen disparate business segments to agree with each other on resolution priorities (everyone previously argued that their bugs were the most important), and personally running the monthly prioritization and scheduling meetings, my position (but not the work) was eliminated in the next round of layoffs.
Fortunately, I found a position back in the IT department where I could properly contribute with my natural skillset for the remainder of my career, but unfortunately, the person who took over my prior prioritization role in the business unit died of a brain aneurysm a few months later.
-PJ