FIFA has refused to ratify the Portuguese midfielder's £22m move to the King Power Stadium after the paperwork was submitted 14 seconds beyond the August 31 deadline.
World football's governing body last week rejected an appeal from the Foxes, who are now considering taking the case to the Court of Arbitration for Sport.
"I can thankfully report he is training with us. Obviously we are disappointed with the decision by FIFA and the other processes are in the hands of the club. But he is training with us and I speak to him on regular basis during training to make sure he's fully focused on what his requirements are," Shakespeare told reporters.
"Ultimately he's a footballer and he wants to play football and train and he's had to miss out not only on club football but international football and we've tried to keep his spirits up. The camaraderie and the banter is brilliant in and around the changing rooms and I wanted to integrate him as quickly as possible and I can do that now. He's out on the training pitch now which is great for him and great for me.
"Behind-closed-doors friendlies are something I will look at as regards his fitness. I will talk with Adrien and the club about which way to go forward. It would be remiss of me not to plan for the worst case scenario, which is that we don't have him until January. In terms of his fitness we will have a plan in place - and we will probably have a Plan A, B, C, D, E and F so it's something that we will continue to monitor.
"I think it's under review. I will leave it in the hands of the club because it's still a can of worms for someone like me who is just football based, not knowing all the ins and outs. I think I will wait for the club to come back to me and I'm sure the club are reviewing what the options are and until they have reviewed them I will make sure myself and Adrien concentrate on the coaching on the training pitch."
Leicester are back in action next Monday when they host West Bromwich Albion.