To get the best response, you should really post support requests in the plugin support forum.
Regarding your issue, it is possible that you deleted an essential site file that had some infected code inside.
My advise would be to restore your site from a good backup, or contact your host to see if they can help you with a restore from their backups (which they may or play not keep).
When you get back up and running work your way through these resources:
https://codex.www.ads-software.com/FAQ_My_site_was_hacked
https://codex.www.ads-software.com/Hardening_WordPress
For future reference, you should really inspect the flagged file(s) for changes from the original versions, and then try and restore the original version of files. Deletion only works for non core or plugin files, and is usually only a temporary solution unless you take steps to close the original vulnerability.
Good luck!