[KevinH]

As long as whatever app knows how to create a valid epub zip (a special zip with a mimetype attribute uncompressed and first) and does not break the rules of epub or violate the spec, then no problems.

FYI, you might want to spend some time with the Sigil User's Guide and actually work through the tutorials. They will show you how to set external editors that can be launched by Sigil to allow people to add or change to their preferred code editors without ever leaving Sigil itself.

Then no need to post or pre-process by unzipping and doing the special zip back up.

Also, if you do manually delete the NCX outside of Sigil the resulting epub will not pass epubcheck and will not work on most e-readers. You might want to read up on the epub 3.3 spec a bit as well.