It’s hard to say without working with the model.
My guess is the model was rendered onscreen with unsaved Style changes when the Scene was created or previously updated.
If you chose, C - Do Nothing, back then, the Scenes and Styles Warning will pop up again unless you just happen to have switched to the Style saved with the Scene.
You’re building a rather complex model whose Styles are controlled by Scenes.
There are multiple ways to add and/or update a Scene.
It’s not clear exactly how you’re going about creating / updating them.
• View > Animation > …
• Scene Tab Context Menu > …
• Scene Manager
The best way to see, understand and control things is via SketchUp’s model mangers.
Create and manage Scenes via the Scenes Manager.
Keep the Styles Browser-In Model panel open as you’re creating/updating Scenes.
The same applies to other managers whose features you may be using and whose properties are saved by a Scene.
Ex. Layers or Fog
The model manager dialogs are “sticky”; dock them together and you can move them as one.
Experienced modelers usually keep them all out / minimized; except for Entity Info and those in use.
Yes, they tend take up a fair amount of screen space.
Setup a shortcut for Window > Hide Dialogs and you can toggle them all on/off with ease.