Can you please follow these steps exactly?
1. Start yEd
2. Open provided graphml file
3. Run provided node mapping
4. Tools/Select Elements, Tab: Nodes(Select: Data Property, Data Property: some_field, Text: "33MOG1H8ND1B", Match text: Complete, Case Sensitive: True)
5. Notice "Structure View", a set of nodes are marked and selected
6. Close File without saving. !!!DO NOT restart yEd!!!
7. Open provided graphml file
8. Run provided node mapping
9. Repeat exact same search
10. Notice "Structure View" now. No nodes are selected.
If you repeat the exact same steps but substitute !!!DO NOT restart!!! with !!!DO restart!!!, the repeat selection works as expected.