Here's something that anyone planning to customize their packaged theme should read:
http://www.concrete5.org/documentation/how-tos/designers/modify-a-p...

However, you might be able to restore the older files because concrete5 copies a copy of them into the trash folder every time you install a new version of the package. So, make a connection (SSH, SCP, FTP) into your web server and locate this folder:
/SITE_ROOT/files/trash/

Look for a folder name that starts with the exactly same words than the actual current package folder you see in the /packages directory. The trash folder has a bunch of numbers at the end, they just refer to the time when the backup was created.

In that folder, you should find your older files. If you've updated the package multiple times, there might be multiple similar folder names you need to search from but the number after the folder name should point you into the latest backup folder.

But unfortunately these backups might not always work. If you find out that the trash-folder is completely empty, there might be some file-level permission issues on your server. If this is the case, unfortunately all your old files are lost if you don't take regular backups of the whole site contents, like everyone should.

Thanks for the link - it looks like the customizations made to the site were not made in the correct way, so when i updated the the theme they were lost, exactly like the document says.