Anyways, I’ve been told, multiple times actually, that the double-y is a Bad Idea and also when switching branches. I think it was @cscs that mentioned it the last time. Apparently it also causes a lot of strain on the server(s).
Don’t be too dogmatic on this. This comes from arch, and they have unlike manjaros 3 branches, only one repo (yes,they have testing, but that’s only for development).
So, when doing usual updates -Syu is fine, thus recomended.
When swithing branches, one should force database refresh.
cheers
A famous bon mot asserts that opinions are like a–e-holes, in that everyone has one. There is great wisdom in this… but I would add that opinions differ significantly from a–e-holes, in that yours should be constantly and thoroughly examined.
We must think critically, and not just about the ideas of others. Be hard on your beliefs. Take them out onto the verandah and beat them with a cricket bat… Be intellectually rigorous. Identify your biases, your prejudices, your privilege.”
I am pretty sure in 2 things: one should not install critical system components like pacman or libpamac from aur or git;
And switching branches should be done with refresh. For the sake of simplicity i vote for Syyuu in the wiki. Uu does not hurt when not applied and the new users have to learn only one command for all 9 possible cases.
When changing branches ~UP~ (Stable → Testing) neither should be needed.
When switching ~DOWN~ (Testing → Stable) uu is not required, but can be used if one wants to sync with Stable and downgrade the packages. But I repeat this is not required, and may not even be desirable.
IMHO the wonkiness OP describes is because of their sync status and unsupported packages in the first place.
I vaguely remember something similar … but if I recall these were examples of people who otherwise use pamac … and pamac needs something like ‘force-refresh’ from time to time, even if you dont switch branches. But thats another subject.
EDIT for your EDIT.
Without any confirmation … I might tend to agree with the other comment there.
Did the OP switch branches and then sync right after? Or sort mirrors after changes branches?
Because sorting mirrors should be done. And probably would have removed the need for the double y.
(and itself may not have been required if the mirror/sync status was in perfect order beforehand)
Could be. But still, what “sorting”? You change branches so you pull from different url. But apparently you half-do it. Someone should probably write some libalpm overlay.
and also when switching branches. I think it was 
