Just solved the problem myself. In case someone faces the same problem, here is the solution:

  1. Go to your fantastico data directory which can be found in File Manager.
  2. Click on the installed_in_root.php file and simply delete it.

Now, you can reinstall Joomla through Fantastico again.

To use Fantastico to remove an installed script, the first log into cPanel, then scroll down to the Software/Services section and click on the Fantastico De Luxe icon.
On the left menu, click on the script you would like to remove. This will bring up the script information on the right side. Locate the installation that you want to delete and click the remove link. Follow the on-screen prompts and Fantastico will remove the script and database associated with it.

Manually Removing a Fantastico Script
The first thing you should remember to do is get back up for your website files and databases just in case. See this link for more information on how to do that:

–> Create a backup with cPanel

Also when deleting the files and folders related to the script in question, it is a good idea not to clear the trash until you have checked and made sure things are functioning as they should be.

Step 1 – Clear Out Your public_html Folder
[ If you installed it into a specific folder, then you will need to delete that folder only. For example, when installing WordPress, you might put it in the folder called, “blog”. Delete the entire folder with that name, and your job is done.]

Step 2 – Remove the Related Databases

This can be done via cPanel's MySQL database management screen. See this link for more information on that:
–> Setup a MySQL Database

Step 3 – Edit/Remove References in Fantastico
Now you need to remove the script from Fantastico. Login to your hosting account via FTP or cPanel's File Manager, and locate the .fantasticodata folder. Inside of that folder, find the folder that matches up with the script you want to uninstall.

>Delete the file installed_in_root.php.

After this is removed, the script should then be able to be installed in the root of the primary domain or addon domain.

To confirm it has been removed from Fantastico, go log in to your cPanel account, click Fantastico, and now it should not be listed as one of your installed scripts.