Your code should not look at the "UTF-8 flag" anyway, but always use decode() and encode() to decode the input from whatever input encoding it is in, and encode to whatever encoding the output expects.
In the meantime, it sounds weird that substr would (re)set that flag in a way that causes errors in the subsequent strings. Can you maybe post a reduced example (ideally with the source strings escaped)?
Something like the following, except of course that it fails?
#!perl
use strict;
use warnings;
use Encode 'encode', 'decode';
use charnames ':full';
use Test::More;
use Data::Dumper;
$Data::Dumper::Useqq = 1;
my $octets = "This is the raw input string, also containing an umlaut,
+ in UTF-8 bytes: mot\xc3\x96rhead ... and some more text";
my $expected = "This is the raw input string, also containing an umlau
+t, in UTF-8 bytes: mot\N{LATIN CAPITAL LETTER O WITH DIAERESIS}rhead
+... and some more text";
my $string = decode('UTF-8', $octets);
is $string, $expected, "The decoded strings are identical (sanity chec
+k)";
my $part = substr( $string, 73, 9 );
is $part, "mot\N{LATIN CAPITAL LETTER O WITH DIAERESIS}rhead", "We sni
+p the correct part"
or diag Dumper [$part, "mot\N{LATIN CAPITAL LETTER O WITH DIAERESI
+S}rhead"];
done_testing();
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