Well, so I got an answer from hosting provider.
First of all they are saying that I have quite many .htaccess files containing "deny from all", but I can see only one .htaccess file and that one is not containing such a command so will have to ask them where the hell are those other files hidden. (yes, I know they are normally not visible)
Second, they are asking me to provide more info about the script,
how the script works, how and where it was executed from so they can investigate this further..
Hope we will get this sorted soon