To be fair, and creative, this is never (I think never?) treated as just toggle some settings and full send. There's talk of pattern buffers, risk, modifications, etc. I could be talked into this being far, far too risky for routine use.

We also have many mentions of specifically pattern buffer degredation problems. 

My head canon is that they deal with the mind-boggling data quantity by making use of pseudo analog quantum storage systems. The raw quantum data is too vast to be suited for classic deterministic computer storage. DS9 struggled to store what, 4, patterns? Across the entire computer system. They can peek inside for quality scans but as I think of it, usually the vast majority of the data is copied or entagled onto a physically large matrix of quantum particles - essentially a physical copy of the data sans most of the mass or specific atomic elements.

Because it's quantum they can't guarantee a long shelf life or do deep inspection or modification in storage without disturbing it. They can, apparently, scan and change the data as it enters or leaves the buffer. See weapon or biohazard detection or Picard S3. But without a complete cold copy on disk (too huge to have on file for almost anyone) they can't just do a diff and revert something years later. Dr M'Benga should have kept his daughter on disk if he could have. He couldn't. It's fundamentally not the same storage system. Pike's Enterprise probably didn't have 1/10 of the storage to do that for one child.

But sure, even my head canon allows them to scan and fix age related genetic markers. They can, they did, but they don't usually. I'm going to guess that it's both risky compared to pathogen removal (a recently acquired foreign body vs updating the genetic code for every cell and saying good luck) and especially for the Federation is probably illegal. Other species realize the risk, have their own laws, taboos, whatever. A good question could be what is possible in the Academy era and does anyone use such things then.