You asked if it had a negative effect on the plant in general- yes it will stress it in general no matter where you cut it. But that stress isn't going to be the worst thing in the world and obviously won't make it curl up and die or anything.
I think you mis-understood my question." Is pruning and its negative effects, relative to area pruned". I know what fan leaves are and what they do. I am asking if I trim a cola fan leaves, will it effect that colas development directly or have a general effect on the plant as a whole.
Forgetting about the stress, which is easy to do, you have to look at the leafs for what they are- solar panels. Think about solar panels on a roof. Say you need 8 to run at optimal level and have lots of energy, but 2 of them are positioned in a spot that they are blocking the others... So if you rip off the two in the way, you may let light onto the ones it's blocking... but you only have 6 solar panels left now (when all 8 was the magic number to be optimal energy).
Do the 8 fans leaves on the said cola feed that cola directly or does the plant as a whole need eg 100 fan leaves to grow an optimal levels.
I say you are in a bit of a lose-lose situation right now. You'll have to figure which loss is going to be worse.
Here are some points to consider:
* The terminal bud is always the best. It has a hormone preference within the plant. This is worth considering if you are going to de-defoliate it because you may be trying to open up more energy to lower buds... which never had the drive to become big buds and therefore you'll end up with no prime spot (because the terminal bud is depleted).
Correct me if I am wrong but doesn't scrog create multiple terminal buds from what would normally be smaller lower bud sites due to bending.
* The plant transfers energy. That means that even with the terminal bud with a growing preference, energy it generates through photosynthesis can be distributed to other parts of the plant. So in a way, the top bud that's blocking a lower bud may still be feeding it energy.
I get what your saying but without light the energy generated and sent around the plant is irrelavent, the buds will not develope.
* Every leaf you lose is a lost energy generator. Leaf loss to some extent is pretty much inevitable on a big plant but it really should be kept to a minimum. Ideally the shape you grow the plant into will have all the leafs and the budding sites in a good spot so nothing goes to waste. If you ever find yourself deciding it's best to cut a leaf- realize you have messed up to get to that point and it's a desperate measure.
A plant left to its own devices will grow to a naturally beneficial shape for maximum growth, there is nothing natural about a scrog though.