I'm a little confused by what you're asking. Are you asking by the time you remove your heating element and reach inside the enclosure with the temp gun, would the temps be different? If so, possibly, but unless you're letting it sit for a few minutes before shooting the surface area that you're trying to test, it's not going to cool off drastically enough to throw your reading off. That's like if you turn your stove off, the stove is still hot, it'll cool off eventually, but if you shot the temp right when you turn it off it's still going to give you the reading you're looking for.