That should not cause any problem, provided acceleration and braking cycles are moderate. All such high speed trains have closed windows by default. So you do not come in touch with outside air while traveling. Once the acceleration cycle is over and the train reaches a steady speed your body will also travel at the same speed. Due to inertia your body will continue to travel at the same speed, with little marginal force required to counterbalance the friction, wind drag etc.
Acceleration and braking cycles can be easily controlled by the driver. The source of worry is turning. It has been found experimentally that tight turning at high speed leads to a feeling of weightlessness, which in turn leads to nausea in sensitive passengers. The feeling is almost similar to what you feel when the aircraft you are traveling in hits an air pocket and the aircraft suddenly gains or loses altitude.
To avoid that all high speed tracks need to be built with longer turning radius. Moreover there are some other technologies to avoid the discomfiture during turns. One such is micro-processor controlled and hydraulically actuated tilting of carriages during turning cycles.
