After running https://github.com/rhoerr/supee-6788-toolbox fix for patch supee 6788 some routes still go to 404 page.
The fixSUPEE6788.log says for those cases "Admin routes for the module will have to be fixed manually". I don't know how to do that (replace what where).
i.e
2015-11-05T20:48:21+00:00 DEBUG (7): Found affected module: Unirgy_DropshipPo
2015-11-05T20:48:21+00:00 DEBUG (7): Found route tag 'udpoadmin'.
Original route XML:
<udpoadmin>
<use>admin</use>
<args>
<module>Unirgy_DropshipPo_Adminhtml</module>
<frontName>udpoadmin</frontName>
</args>
</udpoadmin>
2015-11-05T20:48:21+00:00 DEBUG (7): ERROR: Unirgy_DropshipPo module route already includes _Adminhtml. Admin routes for the module will have to be fixed manually.
2015-11-05T20:48:21+00:00 DEBUG (7): To be replaced with:
<adminhtml>
<args>
<modules>
<udpoadmin before="Mage_Adminhtml">Unirgy_DropshipPo_Adminhtml</udpoadmin>
</modules>
</args>
</adminhtml>
I'm looking at the config.xml file for this module and it has the changed applied (last code below "To be replaced with").
Thanks!
EDIT: Unigry uDropship modules needed to be updated (as rob3000 answered mentions). In this case the extensions have an automatic updater (system->tools->unigry installer).