can you share file
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you had enabled "render region", which means blender will only render a small selected area, which is probably what that yellow square you're seeing is (since the area is very small, and blender highlights it in yellow)
to disable that, you can go into view in the sidebar and uncheck "render region", or just hit CTRL+ALT+B
oh wow that was it, thank you! im guessing i accidentally hit the shortcut at one point
Alt+H will re show all hidden objects.
The orange dot looks like an origin point to me, not all objects have faces and so may not show in the viewport with something clickable. Weird that it moves with the viewport, could it just be far off in the distance? Does it stay in the same place on screen or move when you orbit/rotate your camera, what about in an orthographic projectipn?
You can also use the hierarchy on the far right in the default layout to see which objects are visible/ hidden and select or delete objects which may not have any visible geometry.
If by appear again you mean un-delete then provides you haven't closed blender the object can be found in the DNA view of the blender heirarchy panel.
im VERY sure its not an origin point, no matter the angle it always is stuck to that specific point, i could do a 180 and its still in the same exact corner of the screen.
all objects are visible, thank you for telling me to check, i keep forgetting to do so.
im afraid i dont understand your last sentence.
Numpad point button makes you focus a single selected object. That could be a reason.
that means?