y[n_] := Evaluate[(y[n] /.
RSolve[{y[n + 2] - y[n + 1] + 0.99*y[n] == ϕ[n], {y[0] == 0,
y[1] == 1}}, y[n], n])[[1]]];
RSolve does not automatically Set the definition of y, so you need to assign it manually. Also, the condition ϕ[0] == 0 in your RSolve seems to be unnecessary.