Don't know why your regular expression is so complicated.

Assuming that all <REF > statements are always complete on a single line...

XML File Before

 
</S></TEXT><TEXT><S Entail="142" s_id="0">
Annan urges return to democracy in <REF C-ENTID="Nepal" EXT="Nepal" ID
+="104" S&#1058;YPE="PROPNAME">Nepal</REF></S>
<S Entail="138-139-142" s_id="1">
UN Secretary General Kofi Annan on Tuesday expressed deep concern over
+ events in
<REF A-CLASS="No-Reference" A-REFTYPE="Entity" C-ENTID="Nepal" EXT="Ne
+pal" ID="105" S&#1058;YPE="PROPNAME">Nepal</REF>
and urged a return to democracy, after
<REF C-ENTID="King Gyanendra Bir Bikram" COMMENT="Coref direction is f
+orward" EXT="King Gyanendra Bir Bikram" ID="100" S&#1058;YPE="APNAME"
+>
King Gyanendra Bir Bikram</REF>
dismissed <REF A-CLASS="Entity-Entity" A-DIR="Backward" A-RELTYPE="Ide
+ntity" A-RESTYPE="Intra" A-TYPE="Referential" ANT-ID="105" ID="101">
the country</REF> 's coalition government and imposed an indefinite st
+ate of emergency.
</S><S Entail="138-139-143" s_id="2">
[download]

perl -pibak -e "s/<\/?REF.*?>//ig" junk.txt
[download]

</S></TEXT><TEXT><S Entail="142" s_id="0">
Annan urges return to democracy in Nepal</S>
<S Entail="138-139-142" s_id="1">
UN Secretary General Kofi Annan on Tuesday expressed deep concern over
+ events in
Nepal
and urged a return to democracy, after

King Gyanendra Bir Bikram
dismissed 
the country 's coalition government and imposed an indefinite state of
+ emergency.
</S><S Entail="138-139-143" s_id="2">
[download]

UPDATE: Also assumes that there are no embedded ">" inside the REF tag