How to restore data after MySQL Upgrade?
Open up an Command Line Window as Administrator. Then, follow these steps

STEP 01 : Shutdown MySQL

net stop mysql


STEP 02 : Get the MySQL 5.5 Data into the MySQL 5.6 Data Folder

cd "C:\ProgramData\MySQL\MySQL Server 5.6"
move data data_empty
mkdir data
cd "C:\ProgramData\MySQL\MySQL Server 5.6\data"
xcopy /s "C:\ProgramData\MySQL\MySQL Server 5.5\data\*.*" .


STEP 03 : Upgrade All MySQL 5.5 Files in the MySQL 5.6 Folder

cd "C:\ProgramData\MySQL\MySQL Server 5.6\bin"
mysql_upgrade --upgrade-system-tables


STEP 04: Startup MySQL

net start mysql


Review These Steps

Give it a Try !!!