$string = "
blah



@QUERY
meaningful data
meaningful data
... etc...
@ENDQUERY

@QUERY2
more data
more data
... etc ...
@ENDQUERY2";

print "string1: $string\n\n";

$string =~ s[(?:\r?\n\s*)+(\@QUERY)][\n$1]g;

print "string2: $string\n\n";'

##</code><code>##

string1:
blah




meaningful data
meaningful data
... etc...



more data
more data
... etc ...


string2:
blah




meaningful data
meaningful data
... etc...



more data
more data
... etc ...

##</code><code>##

Using perl 5.6.1 unless otherwise noted.
Apache 1.3.27 unless otherwise noted.
Redhat 7.1 unless otherwise noted.