Two inspectors and a termite guy failed to observe that my house was completely rotted out underneath one of the bedrooms. On another house the inspector failed to notice a thumb-sized hole that was poked through the roof by a falling limb.
So I wouldn't assume the windows will cause you trouble selling the house.
Agreed! Inspectors can miss all sorts of stuff. I had an inspector say "sliding glass door is stuck. Needs lubrication or roller replacement" and left it at that. If they had pulled back the curtain from the wall, they would have seen a massive crack in the drywall suggesting that the ceiling joist had sagged and was now being supported by the door!
The utility savings in the short term are likely minimal. I typically assume that no single home energy upgrade will save me more than 10% of my utility bill. That may not be the case depending on the condition of your building, the climate, and the upgrade... but seems to be a reasonable assumption for a house with average bills and nothing obviously broken.
If my average monthly bill is $100, I figure that upgrading windows will save me $10 or less per month. $120 per year, $1200 per decade. 3 years is too short of a horizon to justify the cost from this angle alone. Very few upgrades would pass this test, perhaps only going from a traditional electric to heat pump water heater.
It is not reasonable to predict if you will get the money back when you sell that far out either. If the supply of homes exceeds demand in your area, your house
might be able to sell quicker than the house down the street with 26 year old windows. If demand exceeds supply and you can get multiple offers on opening weekend, then the windows may not matter at all. Trying to predict which upgrades matter 3 years from now is too hard. Its a lot like trying to time the stock market!
All that being said, I have replaced windows on a house! The other benefits that I noticed were: temperature stability in the room, reduced noise from outside (that house was near a busy road), reduced dust, and an increased willingness to open the windows when the weather was nice. Prior to window replacement I had to fight the windows open and closed so they would sometimes get stuck. Most were standard size windows that I could get off the shelf at the home improvement store so my DIY replacement cost was a couple of thousand dollars.