print $string;
blah



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

@QUERY2
more data
more data
... etc ...
@ENDQUERY2

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

print $string;
blah
@QUERY
meaningful data
meaningful data
... etc...
@ENDQUERY
@QUERY2
more data
more data
... etc ...
@ENDQUERY2