Using a single regex to substitute the match seems to work:

$my_file =~ s/(input type=\"checkbox\".*?(\w+)\[0\]")/$1 label="$2"/gs;

The only modification I made to your original expression is adding " at the end of the outermost capture group.

In reply to Re: Substituting with match containing newline and space characters by kroach
in thread Substituting with match containing newline and space characters by MorayJ

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