It is obvious that during your Sandakphu Phalut Trek, you will cross Nepal border several times. Actually there is not any visible boundary between India and Nepal, and the entire Trekking route goes side by side of Indo-Nepal border. In Indian side you can see some check post of Indian Army, mainly SSB (Sashastra Seema Bal) which generally track the records of Cars and Land Rover with guests travelling. If you trek, there is no need to entry the record as most of the time, you will pass through Nepal only and believe me, there is nobody to halt you. So, please forget about double entry or multiple-entry visas for Sandakphu Trekking.