Steps to reproduce:
1. Create a new project in 6000.2.5f1
2. Create a new script
3. Add the following code:
[InitializeOnLoadMethod]
static void LoadMethod()
{
Debug.Log("InitializeOnLoadMethod called");
Debug.Log("EditorBuildSettings.scenes length: " + EditorBuildSettings.scenes.Length);
}
4. Wait for editor to recompile
5. Observe the console
6. Upgrade the project to 6000.2.6f1
7. Observe the console

Actual results:
0 Scenes are loaded in EditorBuildSettings.scenes.Length when using [InitializeOnLoadMethod] attribute

Expected results:
All required scenes are loaded in EditorBuildSettings.scenes.Length when using [InitializeOnLoadMethod] attribute

Reproducible with versions:
6000.2.6f1, 6000.3.0b3

Not reproducible with versions:
6000.2.5f1, 6000.3.0b2

Tested on (OS):
MacOS Sequoia 15.6.1