You could avoid the loop within a loop issue if you would loop through the array one time and lookup the hash elements as you go. Instead of doing

if ($fields[3] =~ $key) {
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you can do

if( defined( $coll_key_hash{$fields[3]} ){
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to check if the array element is in the hash.

You didn't provide an example of your data but from your code it looks like it would work this way. Even with the approach of deleting array elements as they are used you would be rehashing (har har) a lot of data.