Hello,
I use the layers differently to you so I have a separate layer for each "category", all my lots for example go into the lots layer and all my trees and plants go into another layer. Like you I occasionally forget to activate the correct layer but have never had a problem moving anything, by dragging and dropping, between layers. This includes lots. I have never worried about where an object or tree is in the world because of a nifty little function called Find in Render.
As I have quite a few lots now and use the layer system to group them all together in one place I find it essential to name a lot as soon as I have created it.
Hope this helps.