Any idea why this occurs with just specific lines -- all created in 2D using the "Line" or Linear Array commands?
With the Selector in 3D mode
, you selected and moved and/or rotated a 2D Object-- either ignoring by clicking "YES" the (other... related) Warning Dialog, or had previously selected "Don't show this message again" when that Warning Dialog comes up.
Warning Dialog comes up to warn us that by moving and/or rotating a 2D Object with the 3D Selector, we are creating another Workplane (Coordinate System) and putting that 2D Object on it and making that Workplane the inherent
Workplane of that 2D Object.
Then, later, with the Selector in 2D mode
, we select one of those Objects that we inadvertently put on and assigned a different Workplane, resulting in the Warning Dialog that you originally quoted.
Safest to set your SelectorProperties/General to that "2D/3D Depending on Selected Object... " option.
You might also try activating the "Safe UCS Mode" option in 3D Selector Properties.
More than likely, if you have a lot of Objects in your current drawing, you have multiple Objects on Workplanes (with inherent Workplanes) that you do not want.
Clean-up of that can be easy-- or more difficult-- depending on how complex your drawing is.