If it is an APO 400mm then there is a chance what looks like fungus on the internal lenses is actually glue deterioration on some elements that are cemented together. This is a common ailment for these lenses. Cleaning doesn't help.
Sigma no longer has parts for these and I don't know anyone who would be able to do the procedure or if it is even worth it.
Fungus will usually first show up on front or rear elements. If what you are seeing is deep in the middle of the tube and can only be seen if you point a flashlight in there, then most likely it is the issue I described.
Usually the only thing it causes is loss of contrast on images, which can be fixed in PP. The samples look good.
See
http://forum.manualfocus.org/viewtopic.php?id=3618