I am in the process of installing and and finishing 3/4 white oak. Currently it is all installed and I was getting ready to sand and finish.

My wife left a window open and unfortunately we had a bad storm, heavy rain and high winds. I walk in the front door and all I smell is a pungent wood smell. Uh oh.

So all under the window was pretty wet. I could see and feel the ends of the boads, where to molding will go, were raised/swollen a little.

I have a fan on it and a dehumidifier in the room. I was going to let it dry out and then sand and finish over it (waterlox + OMU).

Does that sound like trouble - should I just replace the boards that were/are wet? Of course I would prefer not to have to replace them.

they should be fine to sand and finishy once they have dried out, but replacing them may not be a bad way to do, had a similar problem when a roof leaked on some unfinished w. oak, i don't think the wood is so much the issue but the moisture below it , when we tore it out the sub floor was pretty saturated and the flooring was pretty well dry

yup,
it's still wet even though it looks dry.
If'n not too many square feet, tear it out and re=place.