Foo.pod:

=head1 Foo stuff

Stuff about Foo.

=over

=item foo

see L<Bar/foo>

This hack works: L<foo in the Bar manpage|Bar/item_foo>

=back


Bar.pod:

=head1 Bar stuff

Stuff about Bar.

=over

=item foo

this item was referenced in Foo.

=back

##</code><code>##

for f in {Foo,Bar}.pod
do pod2html \
    --htmlroot=file:/ \
    --outfile=${f%.pod}.html \
    --podpath=$PWD \
    --verbose $f
done

##</code><code>##

<a name="item_foo">foo</a>

##</code><code>##

see <a href="file:///home/me/perltestlib/DST/XBase/Bar.html#foo">foo in the Bar manpage</a>

##</code><code>##

<a href="file:///home/me/perltestlib/DST/XBase/pod_problem/Bar.html#item_foo">foo in the Bar manpage</a>