How are you determining that your program is losing data?

You are never going to lose any data when reading from a pipe, even if the system call is restarted. However, perhaps what could be happening is that your syswrite is getting interrupted and not writing all of $buffer. You really need to check what syswrite returns and re-buffer what didn't get written for a future write. Note that $wbytes != $rbytes doesn't necessarily mean that an error has occurred, especially when writing to a pipe. The write can be short if the pipe doesn't have enough space for the entire write buffer. The only return values from syswrite that signal an error are 0 and undef.

Update 1: I'll have to double check if a return value of 0 from syswrite signals an error. It does with the system call write but it might not be the case with perl.

Update 2: A common technique for handling an I/O buffer is as follows:

my $buf;
while (1) {
  my $nr = sysread(IN, $buf, 1024, length($buf));
  unless ($nr) { ...handle EOF or error... };
  ...
  if (length($buf)) {
    my $nw = syswrite(OUT, $buf, length($buf));
    unless (defined($nw)) { ...handle error... }
    substr($buf, 0, $nw, '');
  }
  ...
}
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