I don't think it matters that they are not there in CommSec if...

I don't think it matters that they are not there in CommSec if you want to cash out today for a quick $8 or so profit. Just sell the equivalent amount of existing shares you own and when you get to do your tax return, make sure the cost base shares used are your new allocation. From an ATO point of view, you already own those shares as they are showing under Link. It is up to you as to what shares you have sold. CommSec just facilitates the transaction.

That being said, if you plan to do that, why nominate the new allocation as those that are being sold for your tax records? If you already have MQG shares that have been held for more than a year, nominate those instead to get the 50% discount. The new allocation will simply replace them, but in another year's time the new allocation will also qualify for the 50% discount,