Yep, that was it. I almost always forget to check at the bottom. When I do my habit is to transfer everything up to where it belongs. Doing it this time I noticed that something else was numbered incorrectly, probably on my part. When I renumbered everything I found that not only did I have the Harbor Charts back, but also the SH3 Convoy Route Chart! Since I never use that one I hadn't even noticed it wasn't there! Now I have them all.
Thanks for pointing that out.