Yes, you will need to fix the hole after taking off the ledger board
Easiest way is to use Kerdi-fix
https://amzn.to/2JX8GDq
but you could also thinset a piece of kerdi band over it as well
I know its another tool to buy……But a laser level would allow you to shoot a level line across the top of the first row of tile and allow you to cut and adjust the tile to the laser line, rather than start on the second row of tile
Both ways work well
Bosch laser
https://amzn.to/2qIEV0u