medical certificate never received

I recertified for fmla in march 25 2013 received paper work from doctor april 20 2013 faxed paper work to the office that handles this type of paper work. 3 days later received a email stating priliminary approval. In the mean time I suffer from a chronic condition. And have taken hous off from work but have a vot for everytime I am off. And have provided the supervisor with a. Copy. This is now july 2013 and I receive a letter in the mail stating denial of fmla because they say they never receive the documents. My question can I loose my job. I explain to the hr rep that why would I think that it could be denied. After 90 days have gone by since I fax the information over. I just need to know my legal rights.