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perl -ne '
 if(!/^2/) {
...
# to be doing anything with the rest of 'line2'

join -t '|' file1.sorted file2.sorted  | cut -d '|' -f 2 > duplicates

3     110582 SFCA            4158675309               041414041421
3     060784 NYNY            2125552368               190159204657
3     121906 RANC            9195551234               123401123620

3     110582 SFCA            4158675309               041414041421

3     110582 SFCA            4158675309               041414041421

perl -ne '
 if(!/^2/) {
...
         sort -m - alreadyprocessed >mergeout
 mv alreadyprocessed alreadyprocessed.bak
 mv mergeout alreadyprocessed