Do you use SimPE Vecki? You can export your current sim into Body Shop so that you can have many Vecki sims in your game
I would guess the answer to other question is yes, put the custom content back in the game and the eyes will show once again. I haven't tried it myself but since the individual Sim DNA and the character file is still referencing the custom content I can't see why it wouldn't show up. Normally hair, eyes etc revert to what they have been cloned from hence them having brown eyes.
Quick Tutorial using SimPE (Classic GUI):
Start SimPE, Select Neighborhood Browser from the Plugins tab.
Select the neighbourhood that you want e.g Pleasantview then click open.
Select Sims Surgery from the Plugins tab.
Select the sim, then use, then export. In the ‘Export CAS sim' box click on save and finally close down SimPE.