BEFORE YOU MAKE ANY CHANGES...
1) Save a Copy of the Original
2) Print the BOM and areas that are changing on complex projects
3) Think and Prepare!!! In CAD you can do anything. Not so with a metal part! A revision means that some or all of the machine exists. So THINK!
Hard code holes because they already exist in that spot in the metal part. You now have to work around existing holes.
Make sure dependent parts are redefined in your CAD assembly so they are no longer dependent on any parts you are going to remove from the assembly.
Create new parts with new part numbers if you need a longer part. Remember, you can't ADD material to an existing metal part. A 3 inch metal block can not be made into a 4 inch block. It's easy in CAD, not so easy in the real world of metal and plastic.