I’m in the same situation. Could migrate the Hue Bridge (v2) flawless to Hue Bridge Pro (v3) with the iOS Hue App (very nice job from Philips) 
. Integration into Apples HomeKit again, was also no issue.
Atoms Philips Hue app 7.1.1 for Homey Pro does currently not support the new bridge with an official stable version. The Homey support told me, that the Hue Bridge Pro should be supported in about two weeks. Their goal is it, to automatically fix flow issues due to changed device settings from migration. 
In the Dutch Forum you can find a link to the Beta version 7.1.4 of the Homey Philips Hue app, which should work due to user feedbacks.
I didn’t do the Beta test and I’m probably waiting for the final release. Till then, unfortunately without light automation. – That’s life, should have checked before migration. 
