I don't think we'll ever to get to see a contract between two private companies, i.e. Cunard and Nakheel.
Looking at the original Queen Mary contract (thank goodness one Cunard Queen went to a public body where we are able to see the contract) there is this:
The name "QUEEN MARY" is attributable to the vessel and so far as concerned Cunard authorises City to continue to use the said name upon the Vessel. Cunard hereby assign to City all their right, title and interest (if any) in the said name by way of copyright, trade mark, trade name or secondary meaning. Provided nevertheless that Cunard reserve the right to use the said name upon any of their existing or future vessels.
The only thing with the QM contract is that when the QM was sold the Cunard brand was really just the name rather than the lion symbol we have now.
Purely supposition on my part, but perhaps Cunard assigned the name "QUEEN ELIZABETH 2" and/or "QE2" to Nakheel i.e. without the "Cunard" bit, with the same proviso to use the name in the future if they wished. On the Nakheel website she is referred to as QE2 - perhaps Cunard only allowed that rather than the full name?
Such a clause could easily request the removal of Cunard branding, since the lettering below the bridge has disappeared. That would fit with only allowing her to be called "QE2".
Anyway, just a hypothesis........