Tibet & Mainland China

We hope to travel to Lhasa from Kathmandu in May 2016 and then take the train to Beijing where we will start an 11day tour of China. We are a little confused as to what Visas we will require. We heard that to apply for a China Visa we shouldn't say we are going to Tibet. Is that true and if so why.
We were told to get a Tibet tourist permit in Kathmandu and that would cancel the PRC entry permit but we will need it for touring China.
Please advise the best way of getting around this as we want to take the train from Lhasa to Beijing. We are coming through Kathmandu as we are doing a short tour of India and Nepal.