Well, You have a couple of options. Changing (darkening) the 1×10 stain color would be much easier to do without the poly sealing the wood.
Option #1 – Remove the polyurethane and restain to match the other trim. The most effective way to remedy your situation is to "unseal" the wood allowing another stain to penetrate. This could be accomplished by using a paint stripper and removing just the poly and leaving the original stain intact. Or you could sand the window sills down to new wood and then restain.
Option #2 – Apply a gel stain over the poly to darken. This is rather tough to do. The gel stain will not penetrate, due to the sealer, so it has a tendency of being a little streaky.
To determine your best course of action, use a left over piece of 1×10. If you don't have any large pieces left over you will need to buy some more, 2 pieces 1-2 feet long will be enough. One piece needs to be left unstained and the other stained to match your current color. These pieces will be used for experimentation.
You need to determine if you will be stripping off the polyurethane or staining over it. You might need to experiment on an existing sill. The fresh poly should strip off without much effort as long as a strong paint stripper is used.
(Note – All of this will be easier if the window sills are not installed.)
Now determine the new stain color. You have some choices here as well.
1) Fresh New Unstained Wood – A sample of the darker trim, 6-12 inches long, is need as well as a unstained sample of the 1×10 wood. Take this to a real paint store not Lowes. You need a custom matched wiping or penetrating stain. Most paint stores won't want to do this, it takes considerable time for little profit. Have the clerk sample available stains for a close match then tweak if necessary.
2) Poly Removed With Stain Remaining – Everything is the same as above except the 1×10 sample needs the original stain applied. In this case the new stain color will be applied over the existing, so a custom match is your best bet.
3) Sealed With Polyurethane – This is the least desirable option as it is the most difficult to get good results. In this case you will need a piece of stained and sealed wood for the sampling. The paint store won't custom match a gel stain but might be willing to tweak a heavy bodied penetrating stain. Use this article, <a href="https://www.house-painting-info.com/restain-cabinets.html">Restain Cabinets for a New Look</a>, for ideas and "How To" info about applying a gel stain over an existing wood finish.
As you can tell you need to do some experimenting to find the right stain for your situation. I realize this is bad news, but once a wood stain and sealer is applied it is really tough to undo it.