When the shipyard has some unexpected issue (possibly any of those mentioned in T752 or elsewhere) the shipyard core anchor becomes invisible. The block still exists as it can be placed on and removing and replacing the block simply makes the new one invisible as well. Re-linking the shipyard computer with the shipyard anchor makes the anchor visible again.
This seems to happen after server restarts where the shipyard had a design projected prior to the restart that was not unloaded before the restart.