[Lens] Weird layers behaviour when visualization type is changed for one of them

[jughosta]

Kibana version: 8.3

Describe the bug:

1. When there are several layers added including a Reference layer and user changes vis type for a Visualization layer (for example from Bar Chart to Line), the Reference layer gets replaced with a clone of the edited visualization layer.
2. If user deletes the edited layer, 2 layers will be deleted.

Steps to reproduce:

1. Create a vis with @timestamp field from logs sample data
2. Add a Reference layer
3. Add another Visualization layer
4. Notice that all 3 layers are rendered
5. Change visualization type for the 3rd layer to Line for example
6. Notice that both the former Reference layer and the 3rd Visualization layer now have Line type but the Line graph is not rendered <= expected: only the 3rd layer type changed and graph is rendered properly
7. Delete the 3rd layer
8. Now they both are not present <= expected: only the 3rd layer is deleted

Screenshots (if relevant):

Editing:

Deleting right after editing:

[elasticmachine]

Pinging @elastic/kibana-vis-editors @elastic/kibana-vis-editors-external (Team:VisEditors)

[mbondyra]

Caused by [b29b468] [XY] xyVis and layeredXyVis. (#128255)