If you remove the lower portion of the intake tube you run the risk of living things getting sucked into the impeller. The parents may have chosen the location because of the water flow. It keeps undesireable organisms from being able to attach to the eggs and the movement provides a source of oxygenation for the eggs.
You may be able to purchase a replacement tube, attach it to the filter and move the old one an inch or so to protect the water movement. Most likely doing this will cause the parents to eat the eggs/fry. If you do not do this the only way to save the fry is by hatching and raising them in a separate tank. The process for this is easy to find in this and other forums.
If this is not possible and you want the parents to raise the fry, once the eggs/fry disappear, cover the filter intake with a soft sponge material. Be sure to cover the entire intake tube that is below the water line or the parents may simply lay their next batch above or below the sponge. They want a hard surface for the eggs. That way they can keep it clean.
As soon as the eggs hatch start raising baby brine shrimp for the fry. Again, there are many sources on how to do this. I personally prefer the 2 liter soda bottle method but you will need two or three bottles going to ensure a regular cycling of fresh food for the fry.
Charlie