Endosymbiotic gene transfer moves genetic material from an endosymbiont or its descendant organelle into the host genome, notably the nuclear genome. A transferred DNA segment can remain silent. For a transferred gene to replace an organelle-encoded function, nuclear gene expression must work and its protein must reach the right compartment through organelle protein import. Transfer of DNA and transport of proteins are distinct processes in opposite directions. [ref]
Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus by Sandra Stegemann and Ralph Bock. Introduction, p. 2869, and Discussion, p. 2875: transferred sequences and the additional targeting problem
Gene loss and endosymbiotic gene transfer are different: absence from an organelle genome does not by itself show that a functional nuclear copy exists. Conversely, an imported protein may derive from a host gene rather than a transferred gene. The surviving organelle genome is therefore a partial record, not a complete inventory of either ancestral bacteria or the modern organelle's machinery. [ref]
Origin and Evolution of Plastids and Photosynthesis in Eukaryotes by Geoffrey I. McFadden. “How to tame your symbiont”: losses, transfers, host recruitment and repatriation of proteins
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