Question about flags and warps/shifts

Basically, I have a room with a shift thing in it. It plays a cutscene, gives Juni the highjump ability, and she pops out in another room without the cutscene shift in it. Using another shift it takes Juni to the room before the cutscene room so she doesn't go into the void, and so I don't have to repeat every screen again for ONE room.
The problem is that in the Pre-cutscene room, you can still go into the cutscene room and play the cutscene again.
So how would I make the Pre-cutscene room lead to the Post-cutscene room if Juni has received the highjump ability during the cutscene?

In the manager of the cutscene room, select the "Flag A" circle check-box and then select "Item Highjump" in the dropdown list that gets unlocked, then you use the "Map/Target X/Y" values to the post-cutscene room.
So the next time you enter the cutscene room with the highjump you should enter into the post-cutscene room instead.

I TRY doing that, but it never saves even though I hit save one thousand times.

Oh, that's sadly a problem one of the manager problems. Try using the relative value (Map X/Y) instead of the absolute (Target) or viceversa. And if that doesn't work press Ctrl + E in the editor and paste this in the coordinates that represent the cutscene room:
Flag(A)=Power3
FlagWarpX(A)=0
FlagWarpY(A)=0
Then you change the Warp X/Y values to reach the post-scene room. Hope i din't make it too confusing.

Well, it does something... in the post-cutscene room if you have highjump and hit the shift thing, you go somewhere into the void not near anything else, and in the actual cutscene room if you try to leave you go into the void too, even though there's no shift. In fact, I don't know how to trigger a warp. Do I use shift or something?

 Here is what I'm using:

[x994y1002]
Flag(A)=Power3
FlagWarpX(A)=993
FlagWarpY(A)=1007

(x994 y1002 is the pre-cutscene room. x993 y1007 is the post-cutscene room)

You'll just have to put a normal Warp in the post-cutscene room that takes you back to the rest of the level.

Let me see if I understood your problem correctly: you're in room x994y1002 (pre-cutscene) and you use a Shift that takes you to the room with the Shift that triggers the cutscene (let's call it room A); after the cutscene, which gives you the High Jump Power Up, you end up in a copy of room A without the cutscene Shift (let's call it room B). In room B there's also a Shift that takes you to room x993y1002 (post-cutscene), which has a Shift that takes you to room B, not room A.

Now in order to make it all work correctly, you need the FlagWarp in room x994y1002 (like you already did) and a normal Warp in room x993y1002. This works as long as you only exit room x993y1002 by leaving the screen, not via more Shifts; if that's not the case, you'd probably need more FlagWarps, but I can't tell you exactly what to do without knowing the level layout.

If you have trouble telling the difference between normal Warps and FlagWarps, you might want to search for other topics about Flags.