How do you train someone with one leg so much shorter than the other, it does not touch the floor when standing?
As with any other client, you must start with a thorough musculo-skeletal and/or movement-based assessment (i.e., Reebok Movement Screen) to determine exactly what your client can and cannot do with and without compensations.
And as with any other client, you and your client then determine S.M.A.R.T. (Specific, Measurable, Attainable, Realistic, Tangible) short and long term goals. I suggest you work with your client's medical team to determine exactly what is "realistic."
You don't state if your client's knees line up (one shin is shorter) or if the entire leg is shorter yet the tibia and femur are proportionate or if the difference is more in the pelvis, etc. This is an important consideration prior to moving forward.
Once you determine what the skeletal discrepancies are, you and the medical team can figure out which muscles will tend to be tight and which will tend to be weak.
Beyond that, program design should simply combine common sense and ingenuity. For example, you may decide to use a block or even a small medicine ball under the short leg for certain exercises. Or you may have to work unilaterally more than usual or perform more seated exercises than you would usually perform.
There are no hard and fast rules. Just put the "personal" in your personal training. Good luck!