I'm using the mod 'Vehicle Grid' by Optera to add the grid, but when I mine the Raven, it deletes everything on the grid.

Send a report to the mod who created the grid.
This mod contains the transition between ground and "flying" vehicles. Everything related to other operations related to the grid (including mining) depends only on other modifications and the base game.

thats because the raven item is not "item-with-entity-data" ...

you can change it in another mod, where you add the grid
however I changed it.