Here is something similar to what you are looking for. Perhaps this will help you work out your particular solution. (I have a similar situation, dealing with csv files and not having the very useful modules available to me.) This code replaces commas inside of quotation marks with spaces so I could subsequently use split.

$olds='one,two,"three,four,five","six",seven,"eight,nine"';
$i = 0;
$news = join '', grep { $i++ % 2 ? {s/,/ /g} : 1 } split /"/,$olds;
print $news . "\n";
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Output:

one,two,three four five,six,seven,eight nine
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Update

Original version would delete single word inside quotation marks.