Ok, I'll break it down into simplest terms. I'm going to just use arbitrary numbers and angles, so don't take anything for gospel.
-1: On a stock VX lets just say the torsion bars are cranked 20 cranks from the factory. We all know the VX rides, behaves, and was in fact designed for this amount of torsion in the rods. Lets also say that this amount of torsion gives you 3" of clearance at the wheel well and that the A-arms are deflected 15 degrees downwards. The VX is no doubt supported by this amount of torsion in the system.
-2: On a typical lifted VX lets say it takes 3-4 cranks(turns) to gain each extra inch of clearance between the tire and wheelwell. I've heard numbers all over the place, but usually people crank about 14-15 cranks to get about 3 additional inches of clearance which now brings the total to 6". The A-arms are now at 30 degrees downward lets say since they are what is moving to provide you with that lift. The torsion bar is still supporting the same weight of the VX, but now it is under more tension because you are in effect loading up a spring. Everyone notices this in the stiffer handling of your VX. It's like winding up a catapult. We can all agree that if you keep cranking on your torsion bars, it puts more stress on them the more you crank until they eventually snap.
-3: On a reindexed lifted VX, you are unloading the bars so they are not supporting any vehicle weight. You are then basically pre-positioning your 30 degrees of lift and 6" total clearance into your A-arms. Keep in mind the VX is still not being supported by the suspension at this time. When you put the torsion bar splines back into the A-arms, they aren't under any load yet and if you let the VX down, your tires would push themselves up towards the wheelwells. Here's where the trick comes in. We know from my first statement here that the factory cranked the bars 20 turns to get your VX to ride and behave like they designed. You only have to put those 20 turns back in and it will support the weight and handling of the vehicle. That's the difference. You just don't have the extra cranks in the system so the torsion bars aren't working as hard to put you at the right height. Your 6" of lift is still there since you had already moved the A-ams into place beforehand. The trick with reindexing is that you technically aren't cranking your torsion bars to provide any lift you are just repositioning your A-arms to the lifted angle and using the torsion bars to support your VX as intended.
-4: In cases of extreme lift like mine, I did both. I indexed the bars to gain most of my lift, then cranked the piss out of them to give me even more until I was almost riding on the bumpstops underneath. CVs do not like this by the way. The extreme angles they end up with inevitably tear the boots because as the A-arms move down more, they also move inwards. This pushes the CV cages into the cups and makes them ride where they werent supposed to. It also further compresses the boots on their bottoms and pulls them at their tops(referring to the inners, outers will be reverse). When you keep in mind that the boots are rotating at high speeds, and that the rubber is compressing/getting pulled in each revolution, you can see why lifted rigs tear boots. The same stresses are being applied to the cages and balls within the CV cups. That's another reason lifted rigs should watch their CVs.
Hope things are as clear as dirty water now instead of just clear as mud