Hello Anne Marie,
what is the protein you are trying to isolate? Is it membrane bound or cytosolic?
The problem may have been the high SDS. As you know SDS is a detergent and may have damaged your cell membranes. Thus when you centrifuge you aren't getting a pellet because the membranes are broken up.
You could try running as much sample as you can on a gel and conduct western blot.
You may assess the quantity of protein to load by doing a protein assay. That way you will know if there is enough to see anything.
Usually when I scrape my 6-well plates I never get a pellet ( I use lysis buffer to scrape), and the pellet is cell junk that I throw away anyways. Not sure if you are scraping for the cells, or lysing.
Your Ripa Buffer with 1% SDS is that a lysis buffer? if its just for scraping, I would add extra buffers to make it a lysis buffer and then use a syringe to pass the samples through the needle to lyse fully.
Even if your samples are not that concentrated ( by protein concentration determination), you could easily do protein concentration methods such as vacuum, lyophilization and other protein concentration methods.
Anybody have better ideas?