There are a surprising number of engine-specific portions of the engine/aircraft interface - and modern FADEC engines are deeply integrated into the aircraft systems. Stuff that is very expensive to change if you want to swap to a different engine type.
As Someone Somewhere notes, making the 787 engines 'plug and play' was an initial design objective, the deeper they got into it, the more difficult it became, and eventually the whole idea was quietly dropped. I once asked one of my friends on the 787 program what exactly the problems were that were so difficult to solve - he didn't really answer except to say there were 'a lot'.
When Boeing introduced the CF6-80C2 engine on the 767, the FADEC version wasn't ready, so deliveries were started with the "PMC" (supervisory electronic control vs. full authority electronic control with FADEC). A couple operators wanted the ability to upgrade to FADEC once it was available, so we tried to design in 'provision' to allow future conversion to the FADEC version. In spite of those 'provisions' - it turned out the costs to convert a PMC 767 into a FADEC 767 was going to be well north of a million dollars per aircraft (and that didn't include a similar number for converting the engines). As a result, I'm reasonably sure no PMC powered 767 was ever converted to FADEC - it just wasn't cost effective. And remember, that was the same engine type, just a different engine control system.
Years ago, when aircraft were basically analog and engine control was via cables and hydromechanical controls, re-engining with new, lower fuel burn and/or quieter engines made sense. DC-8, KC-135, and 727s were all successfully re-engined.
But I'm unaware of any successful program to do that sort of re-engine with highly integrated FADEC engines.
No first hand knowledge, but I was told by people 'who should know' that Pratt lost their shirt when they had Douglas install JT9D engines on the DC-10 (originally designed for GE CF6). Northwest refused to buy the DC-10 with GE engines (at the time, the CEO of Northwest allegedly said 'I wouldn't by a light bulb from GE) and was able convince Douglas and Pratt that installing JT9D engines would be a good investment. It wasn't - it cost a rather large fortune, didn't work very well, and I believe Northwest ended up being the only customer.