Seems to be working now. But I did it differently.
First of all, I didn’t replace any of the Agent.exe files. I have the old Agent.7984 folder still. So I pointed the bnet duplicate to the Agent.7984/Agent.exe, and the original to the standard launcher file.
I’m using lutris-fshack-6.21-6, and I’ve disabled both fsync and esync. Not sure if the latter matters.
And I cleared out the cache folder.
What made the difference for me was allowing the bnet launcher to handle the different Agent.exe files itself, and pointing to my 7984 folder instead.
Edit: I also switched to the beta version of the bnet app.
Edit2: I also switched to windows7 in the wine config for the prefix.
Edit3: It got stuck on “Reclaiming space” for all WoW flavors, but closing down the prefix and all running processes, then starting up again with the old Agent.exe first, then the launcher, that solved it. Updates were able to finish.
Edit4: I enabled fsync and esync on the restart, seems to be working.
Edit5: The game can’t be launched at all from the launcher using this runner, though. Crashes at startup, so I have to run the game exe manually through another prefix with another runner.