Steps to reproduce:
1. Open the attached “editorWindow.zip” project
2. Open Tools → Editor Window A
3. Open Tools → Editor Window B
4. Dock both windows anywhere on the Editor
5. Exit and reopen the project
6. Observe the Editor

Actual result: Only window A is docked
Expected result: Both windows are docked

Reproducible with: 2023.1.0a3, 6000.0.75f1, 6000.3.15f1, 6000.4.7f1, 6000.5.0b8, 6000.6.0a5

Reproducible on: macOS Sequoia 15.7.4 (M1 Max)
Not reproducible on: No other environments tested

Workaround: Use braced namespaces for custom Editor windows

Note: Not only was the “Editor Window B” not docked, it was closed when you exit the project