There are a number of ways to craft a regular expression to do this. One is to use look-behind and look-ahead assertions. These make sure the characters surrounding the space character match, but will leave them alone and not include them in the text to be replaced:

$id =~ s/(?<=[a-z]) (?=[a-z])/,/;
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However, the results of any regex are likely to be spotty. If instead you use a module like Text::CSV to parse your csv files, you should be able to receive your data clean with all commas intact