Economics. There's a pretty big sunk cost in redesigning something like an engine computer to do a major architectural change. That's high volume, high reliability shit that's done by large teams of people and tested to fuck and if you're amortizing that over only a year's worth of cars, you're wasting a fuckton of money.
Timeframe. It takes us years to bring shit to market where I work, and we're a small shop doing relatively simple shit in comparison. I'd imagine developing a new model ECU takes many years. By the time the design of a new temporary ECU is qualified and production ready, a chip shortage could be over and done with and the thing might never go into production anyway.
Plus there's scheduling. You're pulling together an engineering team to do that job, that would ordinarily be working on the engine computer for the next model, so you're potentially fucking over the release date of a new model car. Retiring one car, using up the remaining parts to build the last of them, changing over the production line, starting up the new model etc is all planned years in advance and "hey lets make the ECU team design this other thing that'll only get used for a year" could toss a wrench in that whole thing.
Generally auto manufacturers just used their corporate might and long term contracts to buy parts and shortages were never an issue. GM/Ford/whoever signs a big contract with Freescale or NXP or whoever, they set aside the fab capacity and they're guaranteed parts, and it's always worked. It's only in recent years when semiconductor companies have merged/gone fabless/whatever, and now you've got multiple chip manufacturers fighting for capacity at foundries, that this shit has even been an issue.
Part of my job is keeping old designs going. We buy thousands of chips when they go EOL so we can keep making the old board. Occasionally we'll redesign a board to change 1-2 parts but we're still keeping the engineering time at an absolute minimum - why? because we're busy designing that whole product's replacement and when we've got that done, the old product fucks off and its old chips and their availability issues are never a problem again.