I'm not sure if this is a CSpace problem or a xIR web app problem or both. I suspect it's a web app problem in not correctly submitting the CSpace 5.0 row IDs (forgive my terminology), and that CSpace 5.0 doesn't know how to deal with repeating values that lack the new CSpace 5.0 row IDs.
I had a series of about 40 objects for which I needed to change the field collection place from "Rome (modern city), Lazio, Central Italy" to "Padua, Northern Italy". Unbeknownst to me at the start, a few of these already had "Padua, Northern Italy" as a non-preferred term for field collection place.
I used the Group Info Review to effect the changes. The xIR informed me that some of the objects already had the desired PT as a NPT, so the term would be duplicated. So far, this is all expected behavior.
Then I opened up all of the records to start removing the incorrect "Rome (modern city), Lazio, Central Italy" rows from field collection place. What I found was CSpace showed the desired term in row 2, and the incorrect term in rows 1 and 3 (see attached screenshot). I expected the exact opposite.
So the term I had just submitted as the new PT was shown in CSpace as a NPT. Weirder still, the term I had just submitted as the new PT is displaying as the PT in the xIR web apps (despite being in row 2 in CSpace).
I suspect that the xIR web apps aren't submitting the correct pos/row information to CSpace. I also suspect that CSpace 5.0 doesn't know how to deal with a pos=0 designation anymore, and somehow this pushes the new PT to the second row. As for why the wrong term was duplicated, I'll just ignore that for now, as I didn't snapshot the records before doing this update. If that's a problem, too, I'll research it and will create another Jira for it.