As per title, it isn't mentioned in the changelog so I'm assuming it isn't intended. Loading an existing save in singleplayer with multiple merged chests nets this popup.

http://puu.sh/BCx7H/3b068d62d9.png

I did have some chests that were 33 high/long, they survived.

Looking at the settings, it looks like the default size has changed from 42 to 40. So anything above 40 gets deleted with content.

Yes, that is not intended change. I'll wait a while with fix (to see if more bugs appear) for this issue since it can be fixed on your side by increasing max chest width/height.