Hello,
I would double check to make sure that all versions of that older domain were redirected, the www and non www, http and https, make sure they all are redirected to the same one.
Make sure that nothing has been done with the redirects in any form, I don't know if anyone else has access to these redirects, but it's very easy for someone to of done something.
Also make sure that these are actually being indexed and Google isn't just having some weird rankbrain fart with the pages it's cached, as I too did a redirect / redesign in march abouts and have been awaiting 700 pages to go bye bye from indexing, however we're down to 659 now, sometimes this number goes up sometimes it goes down a few, but nothing wild.
So when you do a site.domain.com search, Google might show you 100+ pages, but click towards the end of them and see if Google shows you the results or if the page count actually decreases and nothing is shown, this would mean that the pages are just cached and on the road to being forgotten.
Google will keep caches for a bit, in case of an opps moment or even hack attack recovery.
But from 78k to 89k seems like a big jump, but if you had 400k pages to start with, and when you do a site:domain.com and if the last group of pages return nothing, there is a good chance this is just Google's url caching dreaming of electric sheep...