This seems like another common sense vs rulebook debate. Yes any clearance given overrides the last one, and a good controller will specify the restriction within the new clearance, especially if there is a safety reason behind it. But as this is not always done, I would suggest the use of common sense and adhere to the old restriction given, rather than quoting the rulebook in a subsequent incident investigation.
This kind of answer tends to upset a lot of controllers and I am yet to understand why. The basi rule is, as Findo said, if in doubt, ask.