Why are my buildings and zones completely disappearing in Cities Skylines?
Solution 1:
There seems to an issue with assets being renamed when updated:
http://community.simtropolis.com/forums/topic/69058-massive-population-drop-after-update
themes will become 'corrupted' in case of renamed updated assets (not corrupted as in broken, but corrupted as in missing all assets that were renamed).
The solution seems to be unsubscribing/resubscribing - although, it seems that you will still have a population drop but the buildings will regrow.