Hi leee4855,
I am assuming here that - your mother-in-law has a valid will, that there is no issue or you have already obtained probate grant in QLD jurisdiction, the portfolio of shares are all shares in Australia and are shares of ASX listed shares only no private company shares, you have a general power of attorney as attorney of your brother-in-law with no relevant restrictions, and that your mother-in-law’s assets are all in her own name and not in some form of trust. If any of the assumptions are not correct, the answers below may be wrong.
Your question has 2 parts:
Q1 - “… my brother-in-law is disclaiming the shares but not the property, is a letter of transfer sufficient?”
Given the only portion of the estate your brother-in-law wishes to disclaim does not include any real estate, it is assumed there is no stamp duty nor landholder duty issue. In theory, if there is a letter signed by your brother-in-law clearly in writing saying he wishes to disclaim the shares but not the real estate, it is likely sufficient for estate administration purpose. It is not usual though - usually there should be a formal deed, in the event of an audit By ATO etc. A simple deed or more formal deed of family arrangement is recommended.
Q2 - “I am … executor … also the POA for my brother-in-law. (Can I) sign on his behalf to facilitate the transfer”.
You are married to someone who stands to inherit more by signing a document on behalf of another under a power of attorney, while also being the executor. If you really need to you should have clear written record by your brother-in-law saying he wants you to sign on his behalf, and only if there is no dispute whatsoever between your wife and brother-in-law. But unless there is no choice it is not recommended at all.
Good luck!
-Nighthelyn