remove all the referenced nodes from kosovo:
grep ref kosova.osm | cut -d\' -f2| sort -u | grep -e [0-9]> reffed.txt

get all the deleted from my file :
grep delete test2.osm > deletes.osm

now try and run this for one hour:
grep -v -f reffed.txt deletes.osm > unreffed.osm

ok that took too long, write a perl script :
perl removereffed.pl reffed.txt deletes.osm > noreffed.osm

add the header and footer (xml) to the file
cat headerks.psm noreffed.osm footerks.osm > todo.osm

here is the perl script :
UPDATE: moved code out to :
http://bazaar.launchpad.net/~kosova/%2Bjunk/openstreetmapkosova/annotate/head%3A/CleanDelete.pl

testing in progress
osm.org/api/0.6/changeset/2027222