Floor boards still have stains in the soft grains. It will need to be sanded out if, you want a lighter look. The end joints will be tricky. You may not be able to remove stains from there, depending on how deep the stain penetrated.

"He agreed to resand and we are going to go with a water based primer/finish to avoid another stain issue."

I hope this "primer" isn't going on before the stain, to make it more uniform. Using water based finish isn't going to fix your issue. What it will do is avoid introducing an amber tone one can get when using oil based poly.

Proper sanding, staining and wiping is the way to avoid a blotchy stain job. To avoid an expensive mistake, get another sample with the color you chose, to make sure you're not basing your decision on the first sample, that may not have been accurate. If it wasn't sanded as smooth as the floor, the floor will turn out lighter than the sample.

I see no point in sanding your floor excessively to remove stain in the soft grain since you're going back with stain.

We are not going back with stain. We are using easyprime and Loba finish so the stains in the grain will be visible.

Now I get it.

Red Oak has a lot of grain. I'm not sure if the stain in the grain could be removed without removing a lot of wood on the surface.