There is a readme.txt file in the wallet zip and it says the blockchain data is, indeed, stored in %appdata%\intensecoin.
Blockchain data for the new wallet is located in
C:\ProgramData\intensecoin\
You should see a folder labled IMDB that is where it is housed.
Better correct the readme.txt file, then. Honestly, I don't know why wallets insist on putting the blockchain data somewhere besides where the executable is located. It just makes backing up the data a lot more tedious and leads to confusion like @ayers experienced.