Both societies and individuals are grown instead of constructed. If you find a toe is unnecessary, you can't just cut it off without causing more problems than you solve. Parts are not hot-swappable, and if you turn it off, you'll find there's no on switch, so it just stays off. Just let it grow as it likes, more or less.
We could fix it with genetic engineering, but we don't understand enough of the flesh. Even if we did, the map we would need for navigation would be measured in acres. There's an enormous amount of relevant detail. Can't make it any smaller without making key details microscopic. Technically it's possible - ref: Turning completeness - but we can peg this map in the quadrillions of dollars or something of that nature.
By contrast, societies are easy. Like, childishly easy to engineer. They're still grown, but if you want to make it grow differently it takes a very sub-human level of care. Peak performance is not required. In other words, allowing your society to decay is simply unnecessary. Once you realize stuff is breaking more than growing you can just...not. If you really wanted to.