I found this fix on the Sporeum Forums:
If your creature disappears:
1) Go into your creature folder where the .png images are stored and remove the creature in question to another folder.
2) Restart scc.
3) Exit scc.
4) Put the original .png file back into creature folder.
5) Restart scc
6) Go to sporepedia, your creature should now appear in the "Everything" tab.
7) Edit creature (make a small change and change it back to original, eg. resize something)
Save creature, should now appear in your creature section.
9) Make sure you have two copies of the same item, Delete old creature.