I may have misread/understood your code, but in order to be able to open and lock file1 wouldn't it have to be:

copy "file1", "file2"; # instead of move
my $fh = new IO::File("file1","w")
flock($fh,LOCK_EX) or die "can't get lock";
my $fh2 = new IO::File("file2","r");
#read fh2 write to $fh
flock($fh,LOCK_UN);
# perhaps delete file2
[download]

With the rename, even if we could create a file1 to subsequently lock, wouldn't there'd be a small gap where a program could attempt to get read access to file1 and find it not there...