If I remove my heatsink to look at the cpu will the bond from the thermal goo they use be broken?

Most likely.

You might have to reapply thermal paste when you put it back on.

I wasnt shure and I lifted the black clip with raised it about 2cm do you think im safe and it will get hotter and need to be rethermaled. (is that a word)

Your best option is to try it.

If the Xbox just shuts down, then it probably is overheating. (actually, it turns off, but keeps running the fan)
If it doesn't, then you are fine.

If you have a dashboard that lets you view the temp, then you can check to make sure it's running within the normal operating temps.
(I think something like 45 - 60C..not sure. you might want to check.)

Eitherway, it'll turn off before wrecking anything...