Some thoughts on my workflow:
- In Lightroom's preferences, you can change a setting so that it will send the file to Photoshop as a PSD instead of a TIFF, and it will subsequently be saved as a PSD. If you're going to be saving layers (and if I'm working in Photoshop, I probably am) then the layered PSD is likely a smaller file size than the equivalent layered TIFF. I don't know if PSD has other benefits over the TIFF.
- If you're saving your file as a PSD, make sure you have the "Maximize Compatibility" turned ON in Photoshop's preferences. This will allow Lightroom to read the saved file for the purposes of displaying the preview and exporting. It makes the filesize bigger than if Maximize Compatibility was turned off, but it'll still be smaller than a layered TIFF.
- When you save your file, make sure the "Layers" button is checked, especially if you're using the TIFF file type. Otherwise - as you've experienced - it'll flatten the file and you'll lose your layers. Go ahead and let it choose "Save as a copy" if it complains, at least the first time you save it you're saving a copy anyway, it's not going to overwrite the original raw file no matter what you do. (well, within reason of course)
- If you need to re-edit the image that has already been saved as a PSD or TIFF, just go through the same steps as editing a new raw image. Right-click, Edit In, Photoshop. Make sure you choose "Edit Original" and NOT "Edit a new copy with Lightroom adjustments." I know the former works as expected, but I don't know what happens with the latter.
- Once the image is saved as a PSD and showing in your Lightroom library, DON'T try to do any more adjustments to the exposure/colors/contrast/etc in Lightroom. It just won't work right, at least not in my experience. You can crop and rotate, but not much else.
Like Tony mentions, I will save layers but I will usually merge them into "chunks." I sometimes work in dozens of layers but save only a handful of layers in the file. For instance, I was working on removing a table from a poolside and it took me about ten layers to get it right, but then I merged all those ten down into one "fixed table" layer. I also always flatten down any panoramas before saving them or doing further edits.
I haven't used "open as Smart Object" before; I don't know my way around Smart Objects well enough yet.