I’ve isolated the issue in this test app:

XAML

<Window
    x:Class="UI.MainWindow"
    xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
    xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
    xmlns:local="using:UI"
    xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
    xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
    mc:Ignorable="d">
    <StackPanel Orientation="Horizontal" HorizontalAlignment="Center" VerticalAlignment="Center">
        <Button x:Name="MyButton" Content="Button"/>
        <ComboBox x:Name="MyCombobox">
            <x:String>Blue</x:String>
            <x:String>Green</x:String>
            <x:String>Red</x:String>
            <x:String>Yellow</x:String>
        </ComboBox>
    </StackPanel>
</Window>

C#

using Microsoft.UI.Xaml;

namespace UI
{
    public sealed partial class MainWindow : Window
    {
        public MainWindow()
        {
            InitializeComponent();
        }
    }
}

This FlaUI test successfully finds a button, but after picking an item from a combobox it can no longer find the same button:

using FlaUI.Core;
using FlaUI.Core.AutomationElements;
using FlaUI.Core.Input;
using FlaUI.UIA3;
using Microsoft.VisualStudio.TestTools.UnitTesting;
using Microsoft.VisualStudio.TestTools.UnitTesting.AppContainer;

namespace Tests
{
    [TestClass]
    public class UnitTest1
    {
        [UITestMethod]
        public void TestCombobox()
        {
            // Find the app
            var app = Application.Attach("path to UI package exe");
            Assert.IsNotNull(app, "Can't find app");

            // Find the window
            var window = app.GetMainWindow(new UIA3Automation());
            Assert.IsNotNull(window, "Can't find window");

            // Look for the button
            var button1 = window.FindFirstDescendant(cf => cf.ByAutomationId("MyButton"));
            Assert.IsNotNull(button1, "Can't find button the first time");

            // Pick the combobox item
            window.FindFirstDescendant(cf => cf.ByAutomationId("MyCombobox")).AsComboBox().Select(1);
            Wait.UntilInputIsProcessed();

            // Look for the button again
            var button2 = window.FindFirstDescendant(cf => cf.ByAutomationId("MyButton"));
            Assert.IsNotNull(button2, "Can't find button the second time"); // Fails here
        }
    }
}

Is this an issue with FlaUI, or am I misunderstanding something about how the UI automation tree works?