We covered the change to the Google Search Console performance and search analytics reports several times here, where Google dropped the anonymous queries figure from the sum of the overall queries filtered output. This resulted in a ton of confusion and John Mueller from Google said on Reddit, he wasn't exactly a fan of making this change.
To be fair, John did say that the reports are more accurate now and people are better off with better and more accurate reports. But to make a change like this, he knew, would cause confusion and panic. He wrote on Reddit:
I'm not a fan of making changes like this, since it throws people's longer-term tracking off (omg, what happened?!), but I think the new state is cleaner than the old one, so at some point we would have had to make that move anyway.
So the reason he was not a fan of such a change was because of the confusion and because now people have legacy data they really can't reconcile too well. The long term tracking in Search Console has been affected going forward. Over time, in the long run, it will be fine but in the short term, many people who use these reports need to make a mental note that the reports are just different going forward.
John did say they would have made the change at some point, so I guess why wait and just get it over with?
Forum discussion at Reddit.