I am sorry to tell you that if a turtle's shell is soft, it will die unless you correct the situation. The shell is part of the turtle's bone structure. Imagine what would happen if your bones were soft.
The soft bones are due to a lack of calcium. This has two solutions.
First, you must be providing calcium in the diet.
Second, a turtle needs UVB light (direct sunlight) to metabolize the calcium. Sunlight through a window is not direct sunlight. If the turtle is not outside, you must provide a lamp that gives UVB light. Here is a link to an excellent article on lighting.