The moriscos, the muslim descendants that lived in Spain, mostly living in south western spain around the region of granada were subject to multiple programmed expulsion, culminating in the complete expulsion at the beginning of the 17th century by order of the Spanish crown.

Some things to mention, many of them had converted but suspicion never dwindled because some practiced islam in secret. Spain and mostly the region ofValencia suffered heavily from the expulsion, many were skilled workers whose role proved difficult to replace and hit the strained spanish economy who was involved in the wars of Charles V heavily.

In total, around 200-250.000 moriscos were expellend.

Source:

http://www.einaudi.it/libri/libro/lucette-valensi/stranieri-familiari/978880621716 (my uni book)

I think there are parallels with the volatility following the reformation, though that is not ethnic. Also, the Balkans have a recent history of large-scale, violent ethnic conflict, though some of that falls under the 20 year rule and I can't say whether it was state-driven.