Hey! I'm using Twine 1.4.1 and I've run into a problem/bug...I just now opened 1.4.2 Beta 2 and confirmed that the issue is the same there...
...I don't know how to reproduce the bug but basically I have some passages that are offscreen, above the top of the Twine map, and I can't get them onscreen again. I tried Ctrl-A and drag but Twine doesn't let me do that (drag all passages down). I don't see any way to delete the passages either (I can figure out by process of elimination which passages are offscreen, and of course I can open them, but there's no way to delete a passage when editing the passage itself).
Here is a screenshot of what is happening. You can see that I'm scrolled to the top of the map, and that there are two passages *above* the top of the map.
Comments
It certainly isn't a game-breaker, and if it's something really messed up or something (it can't be fixed until like 1.4.3, I don't know) then your game will still be perfectly fine, at least!
I'll bet it was that passage-placement bug in 1.4.1 that placed passages in less than ideal positions after you created a passage from the map or followed Passage>Broken Links>[link]. Which has been fixed in the beta, yay!
1. Edit the TWS file manually in a text editor (like Notepad if on window)
It will be hard to find the relevant values to edit
2. Recreate your story using the SugarCube story format, edit the generated HTML file and then Import it into a new story.
Each tiddler (represents a passage in Twine) stored within the output generated by SugarCude contains an attribute named "twine-position" which represents the position of the related passage within the Twin GUI.
Look for ones that contain negative numbers, and change them to a low positive one, it should work.
Perhaps it would make sense for Twine to reposition passages that are at invalid coordinates? Either that or allow scrolling into negative territory; that would be more flexible but I'm not sure if it would cause problems.
Other than ignoring the issue (which is fine, as long as I don't see it crop up again or in excess), I might try the Sugarcube option, as that seems to involve very little back-tracking!