For some reason though scanning the CDT will actually "stop" the clock. At first I didn't fully understand what was happening so it took me a while to figure it out, but now I've seen it happen a few times so it does seem to be repeatable, either because of some bug or "intended" feature. Here's what I'd suggest doing, go to any Exploration layout base, start on the roof. Scan the first data point, then scan the CDT. The clock will disappear from the HUD. Wait something like 5 minutes or so (enjoy a coffee or something). At this point the clock should have "timed out" if it was simply the HUD clock disappearing but not actually affecting the background "countdown". Yet when you go try to re-scan the first orange data point on the roof, you'll find it's not scannable as the clock timer did not actually "time out" and reset, it's completely stopped until you resume your data point scan. If you drive down and scan the second orange data point, even without re-scanning the first one (which is unscannable because it already counts as scanned), the clock restarts again with whatever incremental timer that data point is assigned (60, 90 or 300 seconds). The first data point however remains "scanned" and does not need to be re-scanned for that run. After the clock is re-started by resuming the next data point scan, if this times out then all of the orange data points will then re-set as usual, but you have an infinite amount of time to get to the next data point after scanning the CDT (unless of course you leave the area and re-enter supercruise in your ship, which I expect would probably reset them). It can be quite a useful "feature" if you use it intentionally to "pause" a difficult data point scan on a high-g world.