This regex /EK(\d+)\D/ captures only the numerics after the EK which is 101 for all the records. Expand the regex to capture the full key (less the last suffix letter if present).

#!/usr/bin/perl -w
use strict;
use warnings;

my @ar1 = qw(
  F40_I_VBBG_RI50-FMVSS301n-2SR424M-HCH-D_01EK101.a3db    
  F40_I_VBBG_RI50-FMVSS301n-2SR424M-HCH-D_01EK101a.a3db 
  F40_I_VBBG_LR50-ECR17p-2SR424M-HCH-D_01EK101g.a3db 
  F40_I_VBBG_LR50-ECR17p-2SR424M-HCH-D_01EK101k.a3db 
  F40_I_VBBG_LR50-ECR17p-2SR424M-HCH-D_01EK101.a3db 
);

my %latest;
for (sort @ar1){
  if (/(.*?)[a-z]?\.a3db/){
    $latest{$1} = $_;
  } else {
    warn "No match for $_";
  }
}
print "$_\n" for reverse sort values %latest;
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