Instead of %words2ids having key-value pairs like

word => 'id'
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they could perhaps be more like

word => [qw{id1 id2}]
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I'm not really across the specifics of what you want. You should supply a sample tagset file, a sample input file, and the expected output using those two files.

My best guess would be changing these lines:

...
$words2ids{fc $text} = $token;
...
s/$re/++$found{fc $1}, "$1 $words2ids{fc $1}"/eg;
...
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to

...
push @{$words2ids{fc $text}}, $token;
...
s/$re/++$found{fc $1}, "$1 @{$words2ids{fc $1}}"/eg;
...
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You should try this for yourself. If you run into difficulties, put together an SSCCE and post it: along with the two sample files and the expected output, this will give us a much better chance of quickly resolving whatever problems you're encountering.

TIMTOWTDI

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11148202
use warnings;
use List::AllUtils qw( rev_nsort_by );

my $corpusfile = '/tmp/d.11148202.corpus'; # FIXME filename
my $wordfile = '/tmp/d.11148202.words'; # FIXME filename

my %words2ids;
{
local @ARGV = $wordfile;
while( <> )
  {
  my ($key, $value) = split /[\t\n]/;
  $words2ids{lc $key} .= " $value";
  }
}
my $pat = do { local $" = '|'; qr/(@{[
  map quotemeta, rev_nsort_by { length } keys %words2ids ]})/i};
my %found;
{
local @ARGV = $corpusfile;
print s/\b$pat\K/ $found{lc $1}++; $words2ids{lc $1} /ger while <>;
}

delete @words2ids{ keys %found }; # not found
local $, = "\n";
print '',"---------------- Not Found:", sort(keys %words2ids), '';
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Outputs:

Lokho udebe <ZUL-SIL-0016-n> kukwenze isilomo.
Ukuzihlola izinyo <ZUL-SIL-0018-n> <ZUL-SIL-0018-n-other> kungahlenga 
+izinyo lomhlathi <ZUL-SIL-0019-n> yakho.
Amakhala agxiza amafinyila.
Ulimi <ZUL-SIL-0017-n> amafutha ulimi <ZUL-SIL-0017-n> wonke ULIMI <ZU
+L-SIL-0017-n> amabheringi.
Sebenzisa amafutha ulimi <ZUL-SIL-0017-n>.
Zama ukugwema ukudla okuncinca udebe <ZUL-SIL-0016-n>.

---------------- Not Found:
ingemuva lomqala
umphimbo
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