Dynamic File Editing

I have a directory for every area code 200-999, and inside each directory is a directory for each prefix that we have added, and one file name 'prefixes' that contains one prefix per line like this '200,0,0,0,0,0,0,0,0'. Right now every 'prefixes' file contains prefixes 200-999, but if we try to enter a phone number without the prefix directory it crashes the system. So, I need a script to check each area code directory and remove all the prefix lines from the 'prefixes' file that don't have a corresponding prefix directory. I hope this makes sense, I am completely lost and desperate for help.

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