Atos and return to work

I am not sure you will be able to help me but I am looking for advice. I suffered a further stroke in Dec 11 and have been on sick pay from my employer. I was sent to Occ Health which just happened to be Atos. The physician found me not fit to return to work and suggested they relook at it in another 10 to 12 weeks. I received a copy of there final report. Then my manager was not happy with it and phoned the dr asking that she changed it. I have now got another report saying that at present I am not capable and should not be placed in stressful situations. I am wondering if my manager is allowed to do this. It seems that without this wording I would have been able to go down the ill health retirement route now the employer is looking at the capability route I am so stressed over it all. Any advice would be welcomed thank you