I know a lot of people (including myself) struggle in keeping an accurate Z zero position between multiple bits. The biggest issue for me is when I am doing 2.5D text in a pocket. Usually, I will have a 1/4" EM doing the pocket clear, then I use a V bit for the letters. I can never seem to get the EM and V bit to cut exactly perfect to get a clean pocket bottom. So, I came up with the idea of using a dial indicator as seen in the picture. I mounted the dial indicator to a linear rail slide to give me smooth and accurate travel. Then I simply hold it in place with a very strong neodymium magnet.
First, I zero to the top of my material with the Z zero plate as normal. After I finish the cut with the first bit, I bring it over to the dial indicator and do an MZ=0 command. Then I slide up the indicator until the dial is set to zero, holding it in place with my magnet. I then move the router over and change bits. Then I move the router back over the dial indicator and slowly jog the router down with the "K" command active, until I get to the zero reading on the dial. Then I do an ZZ=0 command to set the zero point of the new bit. Now, I have an accurate zero point between each bit.
I have only gotten to try this out once on a 2.5D pocket so far, but my first trial worked great. I had a very clean and even bottom in my pocket.