Finally I've done the benchmarks.
And, surprisingly, line-by-line "WHILE()" method in Version#2 wins!
Version#1 consumed 208Mb of RAM vs 70Mb used by Version#2.

Not only it saves a lot of memory, but also it is 20% faster!

My benchmark script tries both methods to read-write 100Mb file in 5 cycles and prints results in milliseconds. Here are the results:

------------------------------------
"ARRAY" BEST TIME :    1.227776
"ARRAY" TOTAL TIME:    6.73529

"WHILE" BEST TIME :    1.103754
"WHILE" TOTAL TIME:    5.71099
------------------------------------
[download]

benchmark script code is:

#!/usr/bin/perl -w
##########################################
#                                        #
#     PURE PERL FILE WRITE BENCHMARK     #
#     METHODS TESTED: ARRAY vs WHILE     #
#                                        #
##########################################
use strict;

my $TEST_FILE_SIZE_MB     = 100;
my $PASSES        = 5;

eval('use Time::HiRes;');
if ($@) {
    error('Couldn\'t load required libraries.');
}

my $file     = "./test.txt";
my $tempfile = $file.'.tmp'.int(rand()*99999);
my $flagfile = $file.'.lock';
my $log;
&testfilecheck;

my $debug;
my ($best_time_array,$best_time_while, $total_time_array, $total_time_
+while);
for (my $x=0; $x < $PASSES; $x++){
    my ($result,$dbg) = use_while();
    $total_time_while+=$result;
    $best_time_while = $result if ($best_time_while > $result || !$bes
+t_time_while);
    $debug.=$dbg."\n";
}
sleep 1;
for (my $x=0; $x < $PASSES; $x++){
    my ($result,$dbg) = use_array();
    $total_time_array+=$result;
    $best_time_array = $result if ($best_time_array > $result || !$bes
+t_time_array);
    $debug.=$dbg."\n";
}

print "Content-type: text/plain\n\n";
print <<EF;
"ARRAY" BEST TIME :    $best_time_array
"ARRAY" TOTAL TIME:    $total_time_array

"WHILE" BEST TIME :    $best_time_while
"WHILE" TOTAL TIME:    $total_time_while
----------------------------------
EF
exit;

sub testfilecheck{
    unless (-e $file){
        open (NEW, ">$file");
        for (my $i=0; $i < $TEST_FILE_SIZE_MB*1000; $i++){
            my $rnd; 
            for (my $y=0; $y < 988; $y++){ $rnd.=int(rand()*9); }
            print NEW $rnd.'|'.time()."\n";
        }
            close NEW;
    }
}

sub use_array{

    my $startexectimemilliseconds = [ Time::HiRes::gettimeofday( ) ];
    my ($debug,$count,$lastline);

    open (DAT, "+<$file");
    flock DAT, 2;
    my @DATfile=<DAT>;
    seek (DAT, 0, 0);
    truncate (DAT,0);
    foreach my $line(@DATfile){
        chomp ($line);
        my $replace = '|'.time();
        $line=~s/\|\d+$/$replace/;
            print DAT $line."\n";
        $lastline = $line;
        $count++;
    }
    close DAT;

    my $elapsedtime = Time::HiRes::tv_interval( $startexectimemillisec
+onds );

    $debug=<<EF;
    method: ARRAY
    exec: $elapsedtime
    count: $count

    $lastline
EF
    return ($elapsedtime,$debug);
}

sub use_while{

    my $startexectimemilliseconds = [ Time::HiRes::gettimeofday( ) ];
    my ($debug,$count,$lastline);

    open (LOCK, "<$flagfile") || open (LOCK, ">$flagfile");
    flock LOCK, 2;

    open (DAT, $file);
    flock DAT, 2;

    open (TMP, ">$tempfile");
    flock TMP, 2;

    while (my $line = <DAT>){
        chomp ($line);
        my $replace = '|'.time();
        $line=~s/\|\d+$/$replace/;
            print TMP $line."\n";
        $lastline = $line;
        $count++;
    }

    close TMP;
    close DAT;
    rename($tempfile,"$file");
    close LOCK;

    my $elapsedtime = Time::HiRes::tv_interval( $startexectimemillisec
+onds );

    $debug=<<EF;
    method: WHILE
    exec: $elapsedtime
    count: $count

    $lastline
EF
    return ($elapsedtime,$debug);
}
[download]

By the way, I've completed several heavy stress tests by launching tens of script instances at once and there were no problems with file integrity. Every script waited until previous instance finish working with the file. Thanks for your tip about using flag file!

Also, I realized that version#2 is more stable against hardware crashes or loss of power. Even if HDD shuts down during write operation, there are always two copies of the file - DAT and TMP, and data always can be recovered from one of them.