Sounds like you are entering clamshell mode.
The color shift sounds like the color profile is changing. Try (re-)selecting your display’s profile from Settings → Display → Color, while your Mac is running in this mode.
I think what’s going on is that when you enter clamshell mode, you’re switching from a dual-display configuration (I assume you are not using display mirroring) to a single-display configuration. So everything is moved to your external display - because the content would otherwise be inaccessible.
And that external display becomes your primary display, because it’s the only one at the time.
When you open the lid, you’re going back to a dual-display scenario. Since the internal display is (I assume) becoming your primary display, all content is moved from the external (previously-primary) display to it. Which is what you are seeing.
If you make your external display the primary display, then this shouldn’t happen. When you open the lid, the primary display will remain the external display and all the windows will remain there. But windows that were on the internal display before you closed the lid won’t move back, because macOS doesn’t remember the previous positions when displays get reconfigured.
I think Display Maid (or any other similar utility) is probably the best solution for you.