Twitch broke up the videos when archived, would they still be accepted as as a run when sent in? If not, is there any way to tell twitch to archive the entire run is one vid?

I've personally never had an issue with Twitch splitting a past broadcast in multiple videos unless there was a connection issue. In that case it is recommended to local record your run and uploading it to YouTube or even Twitch because it is up to a mod's decision to accept your run in that case and if there is a "significant" gap, the run will likely be rejected.