If I have an SCC caption file in Premiere Pro and I make a lot of manual changes in it, can I output

One of two ways. BTW, both now work (PR 2020.2.0) with open or closed captions.

Select sequence in timeline: Ctrl-M (or File -> Export -> Media). Select Caption tab and pick sidecar/scc. If you don't want the video export, just deselect, or use next method.

Select sequence in Project Panel: File -> Export -> Captions. Select scc. 

For both of these methods, the caption stream must be in one layer. It can be cut/moved etc.

Stan