my $rx_altloc = qr/
   ^(ATOM.{9}   # match only atom records
    (.{3})      # capture atom name (and any space included)
    (.)         # capture alternate location identifier
    \w{3}       # match the amino acid name
    (.{6})      # capture chain and residue number
    .+$ [\r\n]) # match the rest of the line
   (?:(^ATOM.{9} # make sure the next line(s) is an atom record
   (?=\2).{3}    # make sure same atom name
   (?!\3).       # make sure different alternate location
   \w{3}         # don't care if it's the same residue type
   (?=\4).{6}    # make sure it's the same chain and residue
   .+$ [\r\n])+) # match the rest of the line
   (?{
      $altloc = $3;
   })
/xm;
...

$file_contents =~ s/$rx_altloc/$1/g;
/xm;