If you get her back into CAS you can fix them.  The NRaas Supercomputer is the mod I use for it, although I'm sure there are others.

I have the same problem with non-controlled sims skipping work/school. 

I'm also having issues with romantic relationships being formed - the only thing non-controlled sims seem to want to do is antagonize each other, with a very few "befriendings" thrown in.  I have seen zero romantic relationships, zero marriages, and the only children that seem to be born are to homeless townies (and after I destroyalltownies, no babies born that aren't forced by me).  No Parthenogenesis! is enabled, but even my already-married couples (with plenty of beds/cribs) aren't spawning by themselves. 

Basically, most of my non-played sims ignore/hate each other and just stand around all day missing school and work 

I have in no way tested this scientifically, but it seems to me that fertilizing with better items (fish, in my case) might make your plants live longer.  I've noticed that plants that have been fertilized with perfect fish seem to live longer than those which are not fertilized, or fertilized with poorer quality fish.  I'm openly admitting that it's not something I'm watching with a magnifying glass, so it could be observer error, but I do think this is what I'm seeing...possibly.

Edited to add that I've also seen the quality of plants increase over time, but I don't know if it's because they've been fertilized (most of my long-term plants are) and/or talked to.  This has mostly happened with my money trees, but I believe I've also seen my apple trees improve quality.

Also, someone long ago in this thread mentioned that money trees don't drop seeds - I've found that they do - rarely, but they do drop seeds.  You just need to keep your eyeballs peeled.

You can also fish up magical gnomes.  Mine always stop working after a couple weeks, as well.