Not sure what to tell you about rectifying the issue. I'll repeat what I've always said - that it is absolutely imperative to Zzero at the exact same XY position when changing tools. Let's say your material is exactly 2" thick and you Zzero on the top of the block. In reality, I would pick a spot on the bed, off the work that I could Zzero to with the plate. I would then pencil in the X,Y coordinate numbers and label it "ZZ here, MZ,2.00 ". Of course you could also zero off the bed and set that up in CAM - but the numbers can be confusing for those who normally work from the top down.

When you ZZ on the table, DON'T forget to MZ,2.00 and ZZ again or it'll be a sad day. If done correctly, this should eliminate all mechanical error in the Z, unless the material moves.

I personally never liked Rest Machining in ANY CAM software. I always make my own vector toolpath boundaries and use those with another toolpath with the smaller tool. In the even't that there IS a step from the smaller tool where it transitions into the rest of the part, it is possible to work a little black magic by either making a component that feathers the toolpath at that lower depth out to the face of the surrounding relief or to modify the SBP. If you used an offset 3D toolpath, it wouldn't be too hard to gradually eek the Z UP every few passes along the entire length of the toolpath. Yes - it's a pain - yes, it DOES work, but it all depends on how much time you have into it and how precious the material is. Just don't move it off the bed until you are TOTALLY sure it's all good. It's also possible to do this at the tool with the nudge command every so often, evenly from the low to high spots. Just creep it up .002" each time and resume. Repeat until it's feathered out.

Another option in terms of recovery would be to just raster over the entire thing .015" deeper with the smaller tool. It'll take a long time, but it'll get you there.

-B