I'm confused, it doesn't sound like she's broody but rather she is laying eggs every day and you are wondering whether you should bring the eggs in after she lays them because you are planning on incubating them, is that correct?
If that is indeed the case, then yes, bring the eggs in daily. After you have collected ten day's worth, put them in your incubator. I say ten days because after ten days old eggs start to lose viability, so it is best to start incubating them before that happens.
Mallards and Indian Runners are both the same species, so there should be no problems with the eggs being fertile.
On the incubator front, it sounds like you need to calibrate your thermometer to make sure it's correct. My favorite type of thermometer for this purpose is the probe type digital ones they make for reptiles, like this:
https://smile.amazon.com/Zoo-Med-Di...s=digital+thermometer+with+probe+for+reptiles
They generally tend to be pretty accurate and are very easily calibrated. To calibrate it, fill a glass half with water and half with ice. Let it sit for a few minutes, and then put the thermometer probe into it. The thermometer should read 32 degrees F. If it doesn't, then you know it's off and can calculate how many degrees off it is. For example, if it says 34 instead of 32, you would know it reads 2 degrees high. So you can use that knowledge to make sure your incubator temp is correct when using that thermometer. In this example, you'd want the thermometer to say 101.5 F when measuring the temp of your incubator, because since it reads two degrees high, you'd know the actual temperature in the incubator was 99.5 F. Does that make sense?