It looks like the answer is hidden in that article, pinning the blame on a faulty water pump. For that to have any bearing it must be too lower water flow causing the log to partially ride along the trough rather than floating in it. Easy to see how a log could flip that way.
When the logs go down the drop and into the splashdown, they are fully riding along a set of rails via wheels on the boats. In the case of the splashdown itself, they ride along a set of raised rails either side of the trough and raised from the trough, which progressively goes deeper into the water along the length of the trough. You can see the rails clearly in the photo below extending from the running tracks on the drop itself. It is only after the splashdown section that the boats actually go back to floating within the trough itself. Having a boat go down a drop and just slam into a full body of water at full speed would not only potentially cause whiplash for riders it could flip the boat due to excessive drag on the front of the boat due to the large amount of water slamming into the boat, this is why they run on the wheels on rails in a controlled manner through the slashdown, gradually lowering the boat into the water before coming off the rails altogether. On almost all water rides with a slashdown, you can clearly see when the boat comes off the rails and gains full buoyancy again. They even modeled it in Planet Coaster on the log flume!
The red bit I have marked is where the boats are travelling fully on the wheels of the boat, the orange line is where the boat comes off the rails, gains buoyancy and is free floating again.
This photo you can clearly see the rails underwater which the boat is riding along, you can also see the side bracing more clearly which stops the boats moving from side to side and extends above the water level each side, they are also visible in the photo above but due to the angle of the photo are less clear.
Remember, the boats use wheels to go down the drops and splashdowns, they only float on the trough sections. This is the same for big slash rides like Jurassic Park River Adventure, Valhalla, Storm Force 10 and every log flume like ride in between!
It is completely safe for a boat to stop mid trough if the water level becomes too low as the boat will just rest on its wheels on the trough. Very safe and no issue or risk whatsoever, it is when the water level becomes too low in the splashdown section where it can become an issue and dangerous, as the water usually acts as the only way of slowing the boat down after the drop. (a very few are aided by magnetic brakes but that is a slightly different ride). Having a lower water level means there is not a way to properly slow the boat down. Resulting in it hitting the water after the splash down at a higher level once it leaves the rails and then going into corners faster causing potential capsizing. The only place they really need to monitor water levels is in the splashdowns as that is the only place there is a real risk of something going dangerously wrong. Notice the wheels in the picture below, specifically the running wheels which are used on the rails of the drop and slashdown like can be seen above.
Someone also mentioned above if a rapids boat could make it round after the pumps were switched off, the answer is usually yes, as the boats move at a rate that matches the flowrate of the water, as the water is literally carrying them. So any water already pumped will flow at the same rate as the boats. Although a low water level can put the boats at risk of capsizing due to the pipes strapped to the bottom of a rapids trough to give the ride the rapids. Log rides can have these too, but the obstructions on the channel base are never wider the the wheels axle width on the boats, meaning the boats can go past safely with no obstruction no matter the water level.
One final thing, have you ever noticed how some water log / splash rides can increase or decrease how wet riders get depending on the weather? This is done by lowering or raising the rails in the slash down by a predefined set amount, to increase how quickly or how slowly the rails lower the boat into the water, thus controlling how much of a slash the boat makes. The amount the rail can move is pre defined and set by the manufacturer to a certain tolerance either way, so no matter if the park have it on the dryest or wettest setting there will always be enough water below the boat to bring it to a safe stop. Most log / splash rides do not have this feature but quite a few do, Including Tidal Wave at Thorpe I believe.