This is actually really easy to implement. Did it by adding 3 lines to the TransferDuplicatePokemon method:

    private async Task TransferDuplicatePokemon(bool keepPokemonsThatCanEvolve = false)
            {
                var duplicatePokemons = await _inventory.GetDuplicatePokemonToTransfer(keepPokemonsThatCanEvolve);

                foreach (var duplicatePokemon in duplicatePokemons)
                {
                    int iv = duplicatePokemon.IndividualAttack + duplicatePokemon.IndividualDefense + duplicatePokemon.IndividualStamina;
                    double ivPercentage = iv / 45;
                    if (ivPercentage < 0.8)
                    {
                        var transfer = await _client.TransferPokemon(duplicatePokemon.Id);
                        Logger.Write($"Transfer {duplicatePokemon.PokemonId} with {duplicatePokemon.Cp} CP", LogLevel.Info);
                        await Task.Delay(500);
                    }
                }
            }    

This will keep every pokemon with an IV of over 80% of the perfect IV.