The fact that you changed the variable associated with package variable %main::foo has no bearing on the contents of lexical var %foo.

use strict;
use warnings;
my $hashref = { "key" => "value" };
my %foo;
local *foo = $hashref;                          # Short for *main::foo
printf("keys=%d\n", scalar(keys(%main::foo)));  # keys=1
printf("keys=%d\n", scalar(keys(%foo)));        # keys=0
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