What are the names of the files that you selected for bulk deletion?
It’s possible that some of them are important parts of WordPress or a plugin, which are infected with malicious code, even though most of the file is ok. If you have the option on some of the files to restore the original, that could fix the file without breaking the site.
It’s also possible that a malicious file is being loaded from part of WordPress, so deleting it could cause an error. Can you check in your wp-config.php file, to see if there are any additional “include” or “require” lines, that should not be there?
There may also be a malicious file loaded from the .htaccess file that gets loaded before WordPress. If you edit .htaccess, you may be able to find it — if you’re not sure what to look for, you can post it here, but use a site like pastbin.com to post it, if you need to (per forum rules), and just post a link to the pasted code here.
