Continuity equation only applies if there is a fixed flow rate. You use it to compare different parts of the same tube, such as the beginning of a vessel and the stenotic region in the middle. It does not apply as readily when you're talking about a complex system with variable distribution between different, linked tubes...which is more like how the human body works.
Here, you are going to think more in terms of current and resistance, more akin to Ohm's law and the other fun stuff we learned way back when discussing electronic circuitry. Raise the resistance in one path relative to other paths, and that path will decrease the amount of current going through it (and other paths will increase). Raise the pressure after a fork point, and more flow will divert into the other channel. If you simplify the kidney into one giant glomerulus, you have 2 main fork points: artery→afferent arteriole/non-kidney flow and afferent arteriole→glomerulus/efferent arteriole. The glomerulus branch always has a high resistance since it's filtering.
Raise the resistance in the afferent arteriole, and flow in the afferent and all downstream forks will decrease; more blood will bypass this area altogether (think of it as less blood flow to your single-arteriole kidney). Thus flow to the glomerulus, or GFR, will naturally decrease. Of note, flow to the 'alternative' fork from the afferent, 'non-kidney flow' will increase.
Raise the resistance in the efferent arteriole and the flow to its alternative fork will increase. In this case, that's the glomerulus. However, since there are now high-resistance areas on both available outflow tracts from the afferent arteriole, overall resistance has increased, and you will probably see some changes to overall flow (distribution in the first fork, afferent/non-kidney) as well.
Basically, you're thinking about this as a linear system, afferent → glomerulus → efferent, but you need to be thinking of it as a FORKING system...afferent → glomerular filtration OR efferent flow
