in their defence, remember it isn't just the kind of people who come here who buy apple devices... it's grandmas and non-computer savvy nouveau rich. the vast majority of apple's customers probably have no idea what we're talking about. i think our use case is very niche and you'd hope anyone savvy enough to need a solution would be savvy enough to find it.
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and you didn't get the ipa from, say, a family member? is google maps in your purchase history? ios and itunes both update apps purchased by a different apple id as long as it is available in the same country as the active apple id, but configurator 2 will not.
I think the fact you had downloaded the updates locally but not transferred them across may have confused matters in this case... it doesn't work like that usually. sorry for the long explanation below but only the full story will illustrate things properly:
I have two apple ids. One for all purchases since I moved to china, and one from back home which I used from, like, 2008 or so. some apps aren't available in china but i still need/want them (mostly a vpn, banking apps etc, in addition to duet display which i don't want to pay for again). my workflow involved having a second user account, and itunes logged into that account. the 10 apps i wanted, were downloaded locally (and these were the only apps i had locally, out of 100s bought). I would then use home sharing to import the apps to my main itunes library, and transfer the apps across to my iphone. for whatever reason (bad luck and forgetfulness, mostly i guess) i hadn't done this for months... i was planning on doing it late this week. the last time i had updated any of these apps was 21 june 2017.
the apps - in their older forms - still resided on my iphone. every app i want which is available on the chinese app store has been kept up to date, but the aforementioned apps aren't available and this had not updated since i last manually did so through itunes. I don't care to switch itunes accounts on my phone after the headaches that has caused me wrt apple music in the past (and having to re-download my entire library). so that was the situation. as an example, i have the .ipa in my mobile applications folder for BBC Sport 1.14.0, the latest version as of 21 june.
when i first used configurator 2 i signed into the "back home" itunes account (because i've been letting ios keep my apps up to date where it can, i have no need to use configurator 2 for my china account) and was presented with updates for 6 of the apps on my iphone - all of which were apps which were unavailable in China and thus ignored by iOS. I did the updates, and now I have BBC Sport 1.16.1 on my phone (along with an updated VPN app, banking apps etc).
If I go to "add apps" it shows every app I have purchased, ever, on that account including apps which AFAIK aren't even in the app store anymore such as FlightControl. I haven't tried to install these, but I can assure you that the list is (or is supposed to be) populated with apps from your purchase history and not from your local mobile apps folder. there are hundreds of apps on the list and they are definitely not locally stored anywhere on my computer.
re: the updated apps for anyone still reading, they didn't touch the copies of the apps still stored in /Mobile Applications. I still have BBC Sport 1.14.0.ipa in there, despite both my phone containing 1.16.1 and the option to add BBC sport to another device saying the version is 1.16.1.
If something has gone wrong in your specific case... it'd be good to find out what.