I scouted around my main city and found a couple of shards. I saved, quit the FE, started again and loaded. All the shards that are behind a fog of war are now hidden so I have to search for them again unless I remember where they were.
ADDITIONAL INFO:
After starting to build on one of the improvements attached to my city, all of these missing resources appeared in the fog of war. So they just aren't properly updated on load.
