I've gone through the process three times now and have been able to duplicate.
Using CCA 2.0 to upgrade a UC with code CME 4.2(0) or 4.2(3) / 12.4(11)XW7 to 7.0(3) / 12.4.2T2.
Ensuring that the apply default configuration button is NOT checked and the clean up flash is checked, at some stage during the upgrade but prior to CCA rebooting the UC the vlan.dat file is deleted. Which can cause lose of connectivity if using anything but vlan 1 to connect to the UC and a resulting upgrade failed message, even thought the upgrade worked.
Apart from having to re-create the layer 2 the upgrade process worked smoothly.
I've searched through bug toolkit and release notes but haven't been able to find any mention of this.