the arcs are text files in c:\program files|city of heroes\missions
you can copy and paste missions within the same arc, or into different arcs.
You just have to be careful with the custom groups and critters. Those are referenced in mission details via indices into a global list at the end of the file. If you copy a single mission out of an arc you need to fix any references and copy the customs into the new file.
And for a while things were cold,
They were scared down in their holes
The forest that once was green
Was colored black by those killing machines
[ QUOTE ]
I hate the fact that everytime I try to save changes it's not saving it to the one that's published so I have to re-publish again making a clone of the mission.
Arghh... friggin confusing MA... 
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I just realized that both dug and myself answered your initial question but not your core issue.
Once you publish your story, it's copied up to the server. The serverside copy no longer references your local files. At that point, editing your local version is pointless - there's no way to propagate the edits to the published version (other than manually recreating them).
You need to edit the published mission instead. If you want to retain a local copy for record keeping purposes (which I always do), you should make your edits, re-publish, then wait until editing again shows that the changes have propagated all the way to the server (which takes a few minutes in some cases). At that point you can do a "save locally" operation to save off a copy of your edits.
Going the other direction - editing locally and trying to push the changes up to the published copy - just doesn't work (other than manual re-creation, as I mentioned). In cases where you absolutely have to hand-edit the file, such as re-ordering details, you have to un-publish (losing all your accumulated ratings) and then publish again from the local copy. If you do that you have to make sure you also copied down any edits you had made to the published copy, since as I said they're not automatically mirrored.
I agree it's confusing. I would have preferred they use the normal web publishing workflow, where you do your work in a sandbox and then push your results to the server, overwriting what's already there.
And for a while things were cold,
They were scared down in their holes
The forest that once was green
Was colored black by those killing machines
[ QUOTE ]
the arcs are text files in c:\program files|city of heroes\missions
you can copy and paste missions within the same arc, or into different arcs.
[/ QUOTE ]
This is all way too complicated for my little brain...
My C-drive missions file only had 2 files in it.
The one I was talking about (one of the almost cloned 'Dream On' missions) and another called 'Autosave' which I remember my other unrelated mission being called for some reason even though I named it 'Fallen Star'.
There are no 2 'Dream On' missions for me to turn my second mission of one into the third mission of the other.
I really hate the technicalities of the MA system.
I'll probably have to just physically add the third mission to one of them the old-fashioned way step-by-step.
Thanks for the input anyway. 
Sorry if this is a stupid question or has been answered before but does anyone know if there is any way to move a mission from one arc to another or do you have to re-do the whole set-up again in the one you want it in?
I made a second mission to one of my arcs and when I went to add a third the 2nd one was nowhere to be found.
So I put the newest one I was thinking about in as the second one instead and after saving it I noticed I was looking in the wrong spot. 'My Published' one had the missing second mish but I was editing in the 'My Local Stories' one which only had one for some reason. I thought they were the same one but not so.
Now I have 2 of the same arc with different second missions and I wanted to transfer the newest one to my published one as it's third.
I hate the fact that everytime I try to save changes it's not saving it to the one that's published so I have to re-publish again making a clone of the mission.
Arghh... friggin confusing MA...