I'm removing files (wordpress theme files )of this site towards the server using cPanel, but nonetheless the files are coming back. The files possess a 000 permissions set.

It's strange that files have proper permissions ( i.e. 777) when they're on my small local machine, but on uploading they're getting transformed to 000. Do you consider the website is infected by virus ? I run an Anti-Virus scan, and located none.

Any reason this might be happening?

If you possess the option, use FTP to handle your server files. It's more reliable than any web-based client.

Otherwise, try altering permissions through cPanel to 777 before removing them. If you're not able to achieve that, contact the server administrator to solve the problem (because it appears like a server/cpanel misconfiguraiton).

chmod 000 declines read, write, and execute permission to yourself, your group, and everybody else.

How would be the files submitted towards the server? Your FTP program might me messing in the files when they're submitted.

For those who have root access you need to have the ability to remove using $ rm -rf filename

Edit

The Umask configurations in your server aren't right. Setting Umask to 777 can make permissions 000.

For those who have spend access you should check for 777 Umask values by running: grep 'umask 777' /etc/skel/.bashrc

If you discover anything alter the Umask to 022. Without having spend access your host should have the ability to fix this for you personally.

Rather than while using cpanel uploader make use of a an FTP program like Transmit for Mac or Core FTP Professional for home windows and make certain to continually use SFTP that is encoded rather than FTP.