In general, although a 'big bang' sounds bad, it's better than a piecemeal migration.
If all the usere are on the same system, you get a good level of functionality. If you split them onto two you limit a lot of features and have to be careful how you migrated users and in what groups you move them.
The best way is to (as you suggest) build a lab system, upgrade, and test whatever functionality is important to your business.
Then when you are happy, simply upgrade 'big bang'.
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These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...