aykutakdemir Hocam ilginiz için teşekkür ederim fakat öyle de olmadı. Sorun htaccess'ten de kaynaklanmıyor gibi. Çünkü eski yedeklerde de aynı şekilde komutla var. Halen daha aynı hata logları kayıt oluyor cpanel'de.
[Sat Apr 21 13:00:44.658395 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.pl
[Sat Apr 21 13:00:44.658260 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.php3
[Sat Apr 21 13:00:44.658210 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.php4
[Sat Apr 21 13:00:44.658150 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.php5
[Sat Apr 21 13:00:44.658048 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.php
[Sat Apr 21 11:21:29.284128 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.shtml
[Sat Apr 21 11:21:29.284089 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.phtml
[Sat Apr 21 11:21:29.283968 2018] [access_compat:error] AH01797: client denied by server configuration: /home/gou/public_html/uploads/index.cgi

Uploads klasöründe index adlı 1 tane bile dosya yok.