If you are talking about the downloads folder for store items that will not show up by just placing the items from the old downloads folder to the new one. You would actually have to have the dcCache folder from your old install. Then all of your old store items will show up. If you are strictly talking about the Mods folder those should not have to be "installed".
This could be the issue.
If you didn't make a backup of your Sims3 folder before uninstalling and you are missing all of your store items, then you would have to get all the .Sims3Pack files and reinstall those. If you downloaded them from here then you need to follow the process for decrapifying them, etc. If you actually bought them from the Store then you can go online and re-download and install from the store.