Here is my file:

<?xml version="1.0" encoding="UTF-8"?>
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="1235" height="650" viewBox="0 0 36.1 19">
<defs>
<path id="s" transform="scale(0.58515)" fill="#000" d="M0,-1 L0.58779,0.80902 L-0.95106,-0.30902 L0.95106,-0.30902 L-0.58779,0.80902z"/>
<g id="s8">
	<use xlink:href="#s" x=".9025" y="0.8501"/>
	<use xlink:href="#s" x="2.7075" y="0.8501"/>
	<use xlink:href="#s" x="4.5125" y="0.8501"/>
	<use xlink:href="#s" x="6.3175" y="0.8501"/>
	<use xlink:href="#s" x="8.1225" y="0.8501"/>
	<use xlink:href="#s" x="9.9275" y="0.8501"/>
	<use xlink:href="#s" x="11.7325" y="0.8501"/>
	<use xlink:href="#s" x="13.5375" y="0.8501"/>
</g>
<g id="u">
	<use xlink:href="#s8"/>
	<use xlink:href="#s8" y="1.705"/>
	<use xlink:href="#s8" y="3.41"/>
	<use xlink:href="#s8" y="5.115"/>
	<use xlink:href="#s8" y="6.82"/>
	<use xlink:href="#s8" y="8.525"/>
</g>
</defs>
<rect width="36.1" height="19" fill="#BB133E"/>
<path stroke="#FFF" stroke-width="1.4615" d="
		M0,2.19225H36.1
		M0,5.11525H36.1
		M0,8.03825H36.1
		M0,10.96125H36.1
		M0,13.88425H36.1
		M0,16.80725H36.1"/>
<rect width="14.44" height="10.23" fill="#002664"/>
<use xlink:href="#u"/>
</svg>

I want to change the fill color of the stars on the flag from black to white using the fill tool. I bring up the fill tool using shift + control + F. I change the fill color from black to white but the color of the stars on the flag does not change. Only the opacity of the stars can be changed. I am using Inkscape version 0.92.4 and Windows 10 Home version 2004. Has anybody else been able to recreate this problem on this file? Thank you.

Saving this as an SVG gives an empty file. Once I got the Inkscape header right it opens.

The stars you want to alter a deeply grouped clones of groups etc. Un/linking/grouping make them objects you can alter in appearance:

Thanks. It worked. I first selected the stars by left-clicking on them. I then pressed Shift + Alt + D to unlink clone. I then pressed Shift + Control + G to ungroup. I then pressed Shift + Alt + D again to unlink clone again and Shift + Control + G again to ungroup. I then pressed Shift + Alt + D one last time to unlink clone. I then pressed Shift + Control + F to change the fill color. How did you know that the stars were linked clones? Is there any way of knowing if and what shapes on a drawing are clones? Which way do you think is the easiest way of knowing what shapes are clones and what shapes are not clones on a drawing? Thank you.

Status bar is your friend:

Thanks. How could I miss the clone statement in the status bar? I will attempt to check the status bar next time. Thank you.

Thanks so much for this. I had exactly the same issue. I am using Inkscape for the first time and didn't realise that cloned objects were linked.