Anyone that tells you a flemish string in general will damage your bow is clueless and/or has alterior motives. Sadly, I've seen this claim made by two different bowyers in their warranty and another used it as an excuse (one of many) to keep from honoring his warranty--even though he supplied the string with the bow.
It doesn't matter which end you twist from--the tension will distribute itself throughout the string.
As the others stated, what you are describing is tiller--twisting the string won't affect that. If the difference is extreme, one limb may have weakened...but again, the string doesn't have anything to do with that.
If the bow is tillered for split and you shoot it 3-under, or vice-versa, you may experience a difference in noise. It won't hurt the bow either way.