The Height Tool was not created to work on individual nodes. It takes the whole set and adapt the height. Anything not on the selected layers will be reset and also marked invalid if you have the mark invalid option on.
You can hack the
AdjustToColliders() to not do the node resets. If you are working with hexa tiles, look in
MapNavHexa.cs else in
Go to the
You will see it has an
if (Physics.Raycast(... and an
else part to that. You want to remove the else since that is what is resetting the nodes.
grid[idx].h = minNodeHeight;
grid[idx].localPosition.y = nodeHeightStep * grid[idx].h;
if (markInvalids) grid[idx].foredInvalid = true;