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The first line is using the same file as input and output. This lead to undefined behavior. Just use a different file as output and process that later one with awk.

You could probably take out the $1=$1 since the input and output field separators are the same.

Try:awk -F\* -vt=`date +%m%d%y%H%M%S` '$1=="ST",$1=="SE"{if($1=="ST"){close(f);f="sample"t"" ++i} ; $1=$1; print>f}' OFS=\| <filename>

Did you try my awk suggestion (https://www.unix.com/302658747-post6.html)? Did that not work?

awk version:
awk -F\* '$1=="ST",$1=="SE"{if($1=="ST"){close(f);f="file" ++i} gsub(/~/,RS); $1=$1; print>f}' OFS=\| infile

--
On Solaris use /usr/xpg4/bin/awk rather than awk

change it into a Perl script that iterates over the supplied arguments eg:

#!/usr/bin/perl

use strict;
use warnings;
for my $filename (@ARGV){
my $file_counter=0;
my $in_record=0;
...