You won't be able to save anything but the Sims appearance themselves in the first step after noting down everything you want to keep. We can cheat in game and use SimPE to get other stuff back.
When you package a lot with Sims to the bin it cuts the connections between the Sims in the neighborhood and the Sims in the binned house. Hence why Dustin no longer knew Brandi after he came back from going to Pleasantview first to go to University. However, EA didn't set up the code that cuts the connections the best. It leaves traces in the forms of memories. Like Dustin's memory of kissing Angela. When you moved Dustin to Desiderata, he know longer knew Angela, but his memory of kissing her still referenced "her".
Each Sim is stored in the game by a unique ID #. Angela may be #30. Dustin may be #24. Memories of things happening to Sims that involve other Sims reference the Sim by their unique ID #. However, that number doesn't note what neighborhood they are from. So there's a Sim #30 in Desiderata Valley and a Sim #30 in Pleasantview. When you packaged the the lot, the reference to Angela was not fully removed from Dustin.
This not fully removed reference is what causes 99% of preventable corruption to spread. Dustin starts telling the world about his kiss to "Sim #30". Which spreads that not fully removed reference around in gossip memories. Which is why some people can go 2 weeks and others can go 10+ years. Just the luck of the draw in what memories were talked about in discussions and how often Sims interact with each other.
So you can't package the Sims you want to save into lots and use that.
It is a doozy to get thrown into researching the options when you realize you've corrupted your neighborhood. At least you caught it before you were unable to load the neighborhood (which may not have happened before you were bored with the neighborhood and wanted to rest it or move on). Keep in mind an option is to fix the family tree now and play the neighborhood until it decides to blow up or until it starts showing signs of corruption. I myself was once in your shoes, but with a family that had been going for 10 generations when I learned what you're learning now.
I'll link a good tutorial for the process of saving the Sims. You can stop after you've cloned the Sims you want in Body Shop. The tutorial is for packaging born in game or made in game Sims in order to share them with other people in a way that removes anything that could cause corruption, so they went a step further and packaged the Sims. Here is the tutorial: https://pixel-trade.livejournal.com/16091.html
I still use this feature today. I like to cheat and see what kids will look like when they grow up without waiting for them to do so. I like to use my born in game Sims as bases for new Sims. The above tutorial is the only safe way to save a Sim to the "Sim bin" like you would in Sims 3 when you went to change their appearance.
The tutorial that Cinebar linked to is an outdated SimPE version and the UI and where things are have changed. But the gist of what you can do in SimPE is there.
