You can't edit the manifest directly. EXT-X-DISCONTINUITY tags usually indicate that the encoding has changed between chunks, for example it has a different frame rate. Are all of the video files identically created, keyframe aligned etc? If you wish, you can
open a ticket and we can take a more indepth look. If the VOD files are available for download then that would help too.
As an aside,
this article has a workflow for creating a smil file containing ABR files. The video files are made available for testing purposes.