Most Peranakan moved to Penang/SG in the last decade, you can see the increasing influence and food sold there. In Malaysia, I am afraid only Melaka is the only place left and even that is lesser due to increasing racism and Islamization. Note that despite marrying Malays, Peranakans are not Muslims as required by "law" in the past.

Source: My gf is Peranakan descendant.

The migration and non-Muslim are originally not a factor to become Bumi/Peranakan. It was simply love between two races back in Melaka. When the NEP started then Arab-isation by Anwar in UMNO decades back, then only the requirement of Bumis = Malays + muslims are set. If the current definition of Bumis are being imposed back in the old days, Sabah, Sarawak and many alliances will cease to be since they won't want that kind of unfair arrangement.