This will keep the first pair found.

my %lookup;
my @to_keep;

foreach (0..$#array1) {
   my $a1 = $array1[$_];
   my $a2 = $array2[$_];

   next if $lookup{$a1};
   next if $lookup{$a2};

   $lookup{$a1} = 
   $lookup{$a2} = 1;

   push(@to_keep, $_);
}

@array1 = @array1[@to_keep];
@array2 = @array2[@to_keep];
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The above will yield "interesting" results for

• @array1 = (1, 1, 4); @array2 = (4, 5, 6); --> @array1 = (1); @array2 = (4);
• @array1 = (1, 1, 5); @array2 = (4, 5, 6); --> @array1 = (1, 5); @array2 = (4, 6);