I wanted to add to this thread.
I have had similar issues this week where members have applied at several church schools but they only show up under BYU Provo for endorsement. In the leader applications it shows a link for endorsement to BYU and one for BYU-Idaho. I was able to endorse a young man for BYU, but he did not show up under the BYU-Idaho application. In the past, it has been an issue with them not completing some part of the process, but in this case I reviewed it with him and everything was complete. So I called BYU-Idaho this morning and talked with a young lady in admissions who said that my endorsement through the BYU application counted for all church schools and they don't use that other endorsement application specific to BYU Idaho anymore. She was able to verify that my endorsement was attached to his application already. I asked if this was true for all church schools and she said yes. (I have someone needed endorsement for BYU Hawaii and there is no link for that so this would answer that question)
If this is true, I would encourage the Church tech specialists to remove the BYU-Idaho link in Leader and Clerk Resources and replace the BYU link with something like "Church School Endorsement" so leaders are not confused and spending time calling the schools to overcome the confusion.
Just a suggestion. If what she told me was incorrect, I would appreciate proper direction from someone.
Thanks!