Help please in merging and copy/pasting from one layer to another

Hello all,

I am preparing a book for publication and initially had all files on one layer. Bad form apparently, but I didn't know better when developing the project. To comply with the publisher's guidelines, I am sorting text, images and overprints into 3 layers: text on layer 1, all images and color blocks on layer 2 and overprints on layer 3. Simple, one would hope.

By and large, a simple cut and paste-in-place + select appropriate layer will move an image file or drop-out text to the correct layer. However, I am repeatedly finding that certain elements simply refuse to meld into the proper layer and become a stand-alone sub-layer with the same layer coloration. When I attempt to merge them into the appropriate parent layer most simply will not do so.

I'm also finding that random text blocks are also deciding that they want to be independent sub-layers which also refuse to merge. 

So, my question, obviously, is: How do you merge all these wayward sub-layers into the parent layers? Simply, I would hope. I am quite mystified why drag and drop in the layers panel is not a viable command. 

Thank you in advance; your help is greatly appreciated.