MySql InnoDB tables are missing after restarting
If you have MySQL 5.6 running before, then the MySQL data is located in C:\Program Files\MySQL\MySQL Server 5.6\data\

If you had recently installed MySQL 5.7, that instance has its own MySQL data in C:\Program Files\MySQL\MySQL Server 5.7\data\.

You need to migrate the data from MySQL 5.6 into MySQL 5.7.

If you are not sure what what version of MySQL was actually running on your Windows Server, here are two things you must investigate:

INVESTIGATION #1


Goto to Windows Explorer
Navigate to C:\Program Files\MySQL


INVESTIGATION #2


For every folder under C:\Program Files\MySQL

Go inside the subfolder MySQL 5.x
Locate the file my.ini



Whichever folder has my.ini was in the installed version of MySQL

If none of them has my.ini, you have to dig a little deeper

INVESTIGATION #3


Click Start -> Control Panel -> Administrative Tools -> Services
Once the Services panel is open, scroll down alphabetically to MySQL.
Right click on MySQL
Choose Properties


This will show you the path to the MySQL binary it called and the my.ini associated with it. If it does not show a my.ini, then the my.ini should appear in the parent directory of the executable.

If this does not work, then you will have to look inside MySQL Workbench for the original connection settings you were connecting with.