Changing bits during a job

Newer Shapeoko user. I’ve been able to run a few jobs successfully that only required one bit for the job from F360. I’m now trying to do a rough cut/finish pass with different bits and this has been causing some issues. First few tries the finish bit was hovering over the work doing the finish passes with about a quarter inch gap. Tried to rezero the z axis with the new bit, but that only resulted in the bit eating into the piece beyond the smoothing operation.
Wondering what I can do resolve this?

For reference I’m using a longer flat mill bit and a fine tip bit, so the bits have a different length.

You will need to re-zero between jobs:


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