Hi James,
When you choose the "Update Nastran" option, it will generate new BDFs with the sized properties as you have seen. However, it does not automatically execute Nastran to generate new results files (OP2); it just copies the latest ones (which are the original, if you have not iterated with FEA). So if you simply size and then update the BDF, but use the original OP2 files, re-sizing will generate the same results.
You can either manually resubmit these updated rundecks to Nastran, or use the HyperFEA tool to automate this process.
Thanks,
Stephen