My suggestion would be to break the file up into brief bits of cutting, each of which stops at a point which can be measured (adding geometry to have a roughing clearance to leave will help this: Making vacuum hose adapters and/or Adding geometry to cut as a pocket with a finishing pass ) — then sequentially cut each file and measure as you go, and reverify the Z before moving on to the next.
Another consideration is that when cutting out the outer profile you should add geometry and cut as a pocket down to tab depth or the penultimate pass.