Sankharas, once eliminated. Do they have a chance of coming back? When I talk of sankharas, I mean the pattern of the mind and the way in which the sanna recognizes an object. After prolonged Vipassana and remaining equanimous to the body sensations, Many of my thought patterns have changed and I can practically see a link there. But theoretically I am still unaware as to how remaining equanimous to body sensations has anything to do with the deepest habit patterns of the mind. 

Now my question is if one stops Vipassana meditation for a sufficient period of time. Is there a way for these sankharas to develop again?
There are ten fetters eliminated in Vipassana meditation. Elimination does not occur before you reach the Sothapanna(stream enterer) state. Until then, fetters are only subdued. Once a fetter is eliminated, it's gone for good. Refer to the table below to know the fetters eliminated at each stage of the path.

Yes, if you stop doing vipassana short of attaining Sothapanna, your mind can fall back to an ordinary corrupted state again.