> Would this affect my own custom

What I did when I migrated was to manually move the existing
custom-set-variables and custom-set-faces from .emacs to the new
custom-file (in my case ~/.emacs.d/custom.el), that way the old
definitions will still be loaded. All new customizations will live in
custom-file. I'm not sure what would happen if the old definitions
were still in .emacs, regardless, a good time to make a backup of
.emacs just in case. Best,
Tom

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