I'm not sure what you mean about new articles showing up in the /uploads folder... That should just be images and other media you have uploaded.
As far as your old images being in a folder on the server, but not showing up...that's because you have missing/corrupt data.
Having the files on the server is a start, but WordPress is totally unaware of them without the database records that go with.
If you have a good .sql backup (and know your way around databases), you could import the backup into a new empty db, and then selectively export from there the tables you want to copy over to your production db.
If that is outside your skillset, at this point you might be better off trying the support for your hosting account and see what backups they have, maybe they can restore your entire site to a previous working version.
In the future, maybe take a look at VaultPress, it's cheap and well worth it.