Does Photoshop create a hidden layer when of the file when it's opened or whenever the Crop Tool is used with the "Delete Cropped Pixels" option checked?
I noticed that after opening a file, if I select the crop tool with "Delete Cropped Pixels" option unchecked and make a crop, that "Flatten Image" is available on the Layers Menu, even though only one layer is displayed in the Layers Pallet? Apparently, there must be another hidden layer, or "Flatten Image" wouldn't be available! In addition, if I click the "X" to the left of the file name to close it, the file "Save" options are limited to only file types that can save multiple layer files. Although, I can access all file types by using the "Save AS" option.
But if I crop the image with the "Delete Cropped Pixels" option checked, and make a crop, that "Flatten Image" is not available on the Layers Menu nor am I limited to only file types that can save multiple layer files when I click the "X" to the left of the file name to close it.
Flatten image does more than merge all the layers, which is why it is a separate function to merge layers. You will find that if you merge layers (Ctrl E) that Flatten Layers will still be available (not greyed out). Flatten is useful if you want to save a number of documents as JPGs after performing edits on them. If you finish with merge layers, it will want to save as a PSD unless you force the JPG. However, if you finish with Flatten image, then it can default to saving as a JPG. So a good way to finish an action you use to batch process a number of images.
Does that help?
It's not a hidden layer. What happens is that your background layer is changed into a normal layer. That is why you can now 'flatten' the image, which will change this normal layer back to a background layer and delete the cropped pixels after all.