Don't forget to save a new Scon file whenever you make new updates.
In my case, for now at least, what I do is:
1- I create a copy of the capx I'm working with,
2- delete everything related to the Scml I inserted into C2
3- insert the latest version of the Scml that contains updates
4- copy paste all events related to the Scml file, from the copy of the capx I created in step 1.
The reason I do this is that, whenever I insert an updated Scml into C2, I get a message telling me that something was still missing (sorry not on my PC right now, can't remember exactly.) But my method works for now, for my needs at least.