Collapsing an Exchange Resource Forest

Good day,

Source: Potentially Exchange 2012

Target: Exchange 2019

Government customer so my access is limited.

Currently, all users and resources are in the target except for their exchange environment which they want to collapse.

With the users logging into the target, Autodiscover is set to point to the source environment.

I will either use Dirsynch, or migration sessions to merge, for the accounts.

when accounts have been merged, I will begin mail synch (synch/switch collections).

My question is: when I either manually switch, or set the tool to automatically switch, will I have to setup CPUU to point to a target Autodiscover (if it is setup)? or should the customer "flip" their autodiscover to point to the new target environment?... and at which point should the do this? How will this affect users that have NOT been flipped? They are keeping their namespace, as a government agency. I just want to make this as painless for the customer as possible.

Thanks in advance.