Re: downloaded sims are not in the Sims 3 download file
The files you download first go in your downloads folder but as soon as you install them, they go into savedSims and if they have cc attached, that goes to the files in DCCache. Houses and households are in the library folder.
There's some stuff that comes on Sims directly, on the files in the savedSims folder, not the download one (those are just the files you've downloaded and later installed) OR in DCCache. All of those should show in your launcher.
If you want them as safekeeping I would either re-download those you want to keep or if you don't know where you've got them from anymore, just export them again from your game. They will then be in the uploads folder.
I don't know why they aren't in your downloads folder anymore but the files in the download folder have nothing to do with what's installed in your game. Those are just backups to reinstall them should you need to.
The backups can simply be moved back into the savedSims folder in your game folder and they should then show up in your game again.
Not certain if that answers your question though.