Hi Simon,
The answer to your question is no and it is because it work like this. When you open with the external app, Intella will export the file from the original evidence source and it will be opened it in its native application (e.g. outside of Intella). Once you have made changes, the external app will ask you to save the file and to choose a file location. That is also outside or, and independent of Intella. The only way to get the file back into Intella is to index it as a new source. There is no file replacement feature in Intella at the moment, but that is on the road map to be added.