I have tried to recreate the problem you are having…in a simplified app.
How are you parenting the cloned light to the appended object? More to the point how are you trying to parent a cloned light to a cloned Letter?
I have have no issue adding cloning a light to the first imported object or even a newly added append of the same letter (not recommended). No reason to append another letter A if one is already in the scene so I am cloning that letter. Then I am trying to parent a clone of an existing spot light to that cloned letter (the second letter A). This is where things break down.
Thats were I am having the problem you are describing…its as if the parent doesnt work.
I can parent it to the append object…no problem…but after that…things get wonky at best.
I have tried parenting groups, lights parented to empties and then parenting the empty, I have tried various things but no luck so far.
If you can show me the puzzles you are using to parent I can try those out.