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s{\[\[(.*?)\]\]}{$1 =~ s/ /_/gr}e

$ perl -Mstrict -Mwarnings -E '
my $x = q{Here are [[a variable number of words]] in brackets};
...
Here are a_variable_number_of_words in brackets
Here are [[a variab]le number [ of ] wo[rds]] in brackets
Here are a_variab]le_number_[_of_]_wo[rds in brackets