A lookahead should do the trick:

use strict;
use warnings;

use Test::More tests => 1;

my $have = 'EST07|E9028;CP392;ALLOC_CP392|R2021||||||||||||0.46458';
my $want = 'EST07|E9028;CP392;ALLOC_CP392|R2021|#MI|#MI|#MI|#MI|#MI|#M
+I|#MI|#MI|#MI|#MI|#MI|0.46458';

$have =~ s/\|(?=\|)/|#MI/g;

is $have, $want;
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