Let me set the question up.

The rebel side selects unique ships for his "fleet" (Y-wing "Dutch" Vander). During a mission he selects to trade out that unique ship with a non-unique ship (Y-wing Gold Squadron). this is allowed in the build rebel squad section on page 7. At the end of the mission one of the rebel effects is to erase the rows of unique ships destroyed in the last mission. The unique ship that was destroyed is replaced by the non-unique with the lowest point value.

So, my question is when you substitute a non-unique ship in for the unique ship in the 200 point fleet what happens to the ship and upgrades when it is destroyed?

Do you erase it even though it was substituted or do you ignor that effect because it is no longer a unique ship?

If more clarification is needed please ask me questions.