Try this:

use Fcntl ':flock';
sub alter_file {
  open(HANDLE1, ...);
  flock(HANDLE1, LOCK_EX)  # exclusive lock
    or die "unable to obtain lock: $!";
  chop; chop; chop;
  close(HANDLE); # also releases lock
}

sub process {
  open(HANDLE2, ...);
  flock(HANDLE2, LOCK_SH)    # shared lock - allows multiple readers
    or die "unable to obtain shared lock: $!";
  ...read from file...
  close(HANDLE2);  # also releases lock
}
[download]

Note: The flock call will block until the lock can be acquired.

Another approach which may work for you is to use an atomic operation to replace the contents of file:

sub alter_file {
  open(HANDLE1, ">/some/tmp/file");
  ...write to HANDLE1...
  close(HANDLE1);
  rename("/some/tmp/file", "file");
}
[download]

In this case no call to flock is needed in the process subroutine. Other processes accessing file may not always get the latest version of the file, but once they open file the contents won't change on them.