There is pretty much no chance at all that this affects efficacy.
Do you have the source for this claim? Linked Anvisa slides page 6 says "todos os lotes" (all lots) had replicating virus.
I agree this is about quality control and it is extremely unlikely to affect vaccine efficacy. (If anything, it would improve vaccine efficacy.)
I don’t think you can say this with much certainty, if the viruses either regained or never lost E1, it’s also possible that the same is true with E3 which modulates immune response.
Also, either of these genes could’ve replaced the Coronavirus spike protein.
Replicant viruses do not carry the spike protein, they don't contribute to antigen protection.
Are you sure? Do you mean that all of them must have had recombination that added the E1 gene and dropped the spike protein?
Considering Slovakia also said that Russia did not deliver a vaccine matching the characteristics of the one in The Lancet, I think those data are basically irrelevant now.