Could someone provide an overview of how the chip design files are used by the fabrication process? What I mean is once the design engineer(s) have completed the computer generated design blue print files for the fabrication process do these special files get read into the machines which fabricate the silicon or the wafer or the die? Can they be easily replaced with an updated version of the finished design files?
Chip making is a process of lithography, i.e printing.
To do this you use masks, which are used to project patterns into Photo-Resist (PR) on the wafer. Sometimes the mask is used to block things, sometimes the mask is used to pattern a layer underneath that is more resilient to the process (a Hard mask). PR can be used in etching or implanting, and many other steps.
You start with a design in which you've laid out the transistors, you will have Well implants, Isolation structures (SONOS, STI), poly-silicon masks (for the gate, note I've just skipped over between 2 - 7 masks depending upon the the process). BEOL (Back End Of Line) masks for metal interconnects etc. and so on and so on.
The layout database is in a data format called GSDII or Oasis. This data is then subjected to a "fracture" process that generates MEBES data which is the data that is sent to the mask shop for generation of the masks used in lithography. In fracture, various things are done, like scaling, and correction for interference effects etc.
Once the data is fractured the designer is asked to verify that the fractured data still corresponds to the actual designed files. It rarely is different. The masks are made, and are typically chrome plating on Quartz. These masks are then checked for perfect fidelity. If they don't match they are then fixed or redone.
These masks are then sent to the fabrication factory and are loaded in the mask storage or the cassette storage which is adjacent to the lithography tool. This has to be kept clean, clean ... clean as even a single spot will replicate on every die produced.
I've glossed over so much here, the details fill shelves of space.
To answer your question about replacement. Yes, you can replace masks in the fab. Indeed, on the first runs through you typically put "stops" at different parts of the process, you start with say 12 wafers, stop 3 at well implant, 3 at poly, 3 at contact and three go all the way through. You test the last three, find a problem, change a mask and then restart the wafers that were stopped earlier.
see this for a little more detail.
Computerized industrial processes run on files consisting of machine-specific numerical commands, like GDSII for IC's, Gerber for PCB's or G-code for CNC machines. Whatever design program is used performs manufacturability analysis on a user's design to make sure that the design is achievable, then compiles the design to the machine-readable format.
Silicon is an element. It is not so much fabricated as dug up where the sand is pure and the labor cheap, then taken to a factory where the it is smelted and purified at high temperature, crystallized, and cut into wafers. The industrial standards are quite rigorous, and a lot of computers are involved in factory control and testing, but the wafers themselves are not designed - their goal is to produce a perfect crystal plate. I doubt design files are involved before the die stage.
Chemical/optical processes are used to make chips on the dies, and here the design files come into play. I do not see any reason why one compiled file could not be replaced with another up to the point when the machine actually performs those actions. Obviously, any changes must leave the new design compatible with any actions that have already been performed, or you might as well throw out the batch. Still, the processes are fast enough that I do not expect the designers to make changes in the middle, unless there is a whole production line for the product. In that case, someone would call in a halt and provide new files. If the process was changed, the limited volume of half-etched silicon may not be worth the effort to salvage, and any half-finished pieces would probably just be thrown out.