I don't see them vanishing, just not being there, initially. I believe they are taking a bit of artistic license with what we are being shown, much as we later see with the Doctor & Churchill in The Wedding of River Song. Just as we see there, there is no visible transition (to us) but we come to understand that the sections of time that are edited out of memory are not being shown to us.
I.e., we are seeing what Amy (in this case; the Doctor and Churchill, in the Wedding episode) remembers, not the actual sequence we would see if we were watching a video tape of the event. Between times we see her unmarked skin and then see it with tally marks, it's implied that she saw them again, made the marks (as explained earlier, a way to log how many of them they've seen), then looked away and forgot them.
It's not totally consistent, tho -- they show us a scene (after 52 seconds) where she looks up and sees them, despite forgetting it a few seconds later. Not consistent, but dramatically effective, as, by this point, we've gotten the fear of the unexplained marks, we know what is going on, and they stop jerking us around :)
- At the start of the clip, she runs into the room. No flashing hand.
- She turns and runs to the door; as she grabs it (7 seconds in), her hand is flashing (and has marks on the back) and she listens to the recording hearing what she has now forgotten.
- 35 seconds; she's run back to the other side of the room. No marks visible.
- 37 seconds; marks on her arms, then she sees them on her face in reflection
- 52 seconds; she looks back and sees them above her.
- 116 seconds; she makes a noise and lifts her hands to her face; it's hard to see, but the tally marks are still there
- 123 seconds; looks down, forgets them, still has tally marks
- 128 seconds; leaves the room -- still has marks.
In response to the observation that she had marks before the included scene, I went back and watched the episode again. I think you are thinking of the marks at the very beginning, which she later washes off.
Going to the start:
- July 1969 opens with Amy running from the men with the body bag. When she falls, she has tally marks on her arm visible.
- Canton then talks to the doctor, showing him pictures of her with the markings.
- River and Rory both have marks when they meet their end (for the moment), but River dives into the swimming pool, and is seen toweling off, so we can presume that her marks have been washed off. At this point, we never really see Amy's arms, so we can't tell if she has any marks.
- At 7:32, Amy and Canton pull up to the Orphanage, both check their palms and see no glowing indicator, and declare 'clear.' I think we can assume that Amy has washed her old marks off at this point, as they would confuse things, otherwise. (This is confirmed by the Flashback a moment later, showing them getting the recorders in their palms, and even Rory has washed his marks off.)
- At 11:19, then enter, and Amy's face and neck are clearly clear of marks. As they walk up the stairs, there isn't a clear shot of them, but what we can see of her hands shows no markings
- Amy then indicates that 'I'll check upstairs'; as she pushes open the door, we can see her hands are unmarked. As she crosses the room, she holds a Flashlight and a cell visible to the camera, in the process, showing both her hands (and wrists, and lower forearm) to be unmarked.
So, it looks like she had no marks when she went in to the scene you included; again, my guess is that you are remembering the marks from the earlier scene, before she 'died.'
If you still doubt, let me know, and I'll add screen-shots :)