No, don't throw any data away. Most is salvageable if you know how.
There are a couple of ways to resolve this.
- Sum combine: If the flat is under exposed and you haven't hit your ADU (which would appear to be the case from the information you've provided - 11,000 with a target ADU of 20,000). If you've got a few subs with 11,000, after subtracting darks, sum combine two of them. In this instance your target ADU will be 22,000. Once you've sum combined the individuals as pairs, you can then median combine the summed pairs to improve the flat accuracy.
- If your flat ADU is not too far off the target, you can use pixel math to resolve this. In its basic form, your data numerical. Don't loose sight of this fact as there are some powerful tools at your aid. Each pixel has a depth based on bit space. If you use pixel math you can increase or decrease all pixel values in an image to reach the desired ADU. This is sometimes known as data scaling, thought I don't particularly like this term as scaling is typically size sampling in the photoshop realm. Anyway, 20,000 / 11,000 gives a scaling factor 1.81. So if you scale the data by this value you will reach your desired ADU. Respectively, you can also downscale if your flats are overexposed.
There are many other uses of pixel math which I'll leave for another day.