There is information that I think would be needed to answer this fully although people could make assumptions and give answers as well.
1) Are the drains full siphon or partial siphon? Which ones or both? How far do the drains fall from the point water siphons to the point it exits? Is it an unimpeded vertical drop or are there bends and constrictions? In short, is it 40mm all the way in and out of the drains to the exit?
2) Is the pump 12,000 lph at zero head or is that the rating you have been told it is at the head it currently sits? If it's the former, what is the rating at the head it currently sits? Is the 25mm return equal to the original outlet on the pump or is it smaller? If the original outlet from the pump is 25mm, is it 25mm all the way to the tank or has it been reduced somewhere?
Providing the name of the pump would help, the actual head and descriptions of the piping size all the way around would also help.
Here's some assumptions however.
1) A 40mm pipe draining at full siphon for only 2 feet unimpeded will pull 30% more than 12,000 lph per hour. Of course, it won't be at full siphon if the pump can't push 12,000 lph to the tank, but that's another issue. If the drains are NOT at full siphon, it will be noisy, but the drains can handle that pump.
2) If the pump is 12,000 lph at zero head, or if the drain falls even farther it will be even more unbalanced. You can get more precise measurements if you identify the pump and the head calculations. You can of course throttle back one of the pipes (if one is set lower than the other) with the right apparatus to get it balanced to whatever your pump can put in the tank.
2) Although the pump is not over producing for the drains, make sure not to constrict the pump. If the outlet is 25mm, the attachments and hose should be 25mm all the way to the tank otherwise if it's smaller there can be back pressure which can negatively affect the pump.
If the pump came with a 25mm outlet, it was designed for that and there should be ratings to tell you how much it can pump at various heads. E.g., it might be 12,000 lph at zero head, 10,000 at 1 foot, 7,000 at 2 feet, etc etc. eventually reaching zero at some height.