Ok so tit for tat , this is done by a malware or virus on your website which creates .htaccess file in every subdirectory of public_html , to deal with it I have prepared a script for hotfix
Create a file in home directory of user (/home/exampleuser) with any name such as fix_malware.sh and copy and paste the below content
#/bin/bash
#This script delets all htaccess files which contain FileMatch keyword
echo "Starting Script"
find ./public_html -name ".htaccess" | while read line ;
do
grep -q "FilesMatch" $line
if [ $? == 0 ]; then
rm $line
else
echo not found
fi
done
after pasting the content make sure to give executable permission to the script file, with command chmod u+x ./fix_malware.sh
and atlast run the script by calling ./fix_malware.sh
.
After the script will finish executing you may see your websites working again, but some of them must be misbehaving because of missing htaccess file , sadly you need to find correct htaccess file and paste at the project desired location .
Note I ran the above commands from home directory (/home/exampleuser) , dont forget to change paths if you are running from any other location.
Hope this helps
Happy Coding