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# today's data -- your starting point
my %SHIPS = (
...
  ],
  # other ships
);

use Data::Dumper;
print Data::Dumper::Dumper([\%SHIPS],[*SHIPS]); # save to file, don't 
+print

my %SHIPS;
do 'dumped_file';

while (<$CSV>) {
  chomp;
...
  $SHIPS{$shipname} = \@arr; # push back
}
# that's you done with the merge