Is the new board skimmed or at any level heigh adjusted relative to Z?
Assuming your Z don’t loose steps, have you calibrated the steps per millimeter (or inch)?
If you command Z to jog 1" is the actual movement = 1"?
If the board is skimmed, steps/mm is right and no steps are lost there is no reason why it should dig into the board.
I have a skimmed board and when I carve material that vary slightly in thickness (thickness is rarely uniform throughout the piece) first “zero” on the board, then jog the bit to a known height (say 13mm if I use 12mm thick stock) and carve down to 13mm depth.