Anything that removes metal - grinders, sanders, mill bits, drills WILL get stuff inside the can with one specific and fairly difficult to achieve exception. The exception is if you grind the top (or saw or mill) to foil thickness and then carefully puncture/tear the remaining foil. Even tearing and puncturing can, but usually doesn't leave flakes inside.
Another feasible approach is using a rolling cutter similar to that used to cut copper pipe to cut through the lid. Not totally debris free but better than most drilling/milling/grinding operations.
Finally, think about the risk of displacing debris that is already inside the can from a harmless location to someplace that matters. Most are fairly clean inside, but not all, and at least some manufacturing processes have a "mechanical getter", a patch of sticky substance to grab and control anything that has found its way in. Getting such hot while shaking and vibrating the package is likely to release any such debris.
The only times I have been involved in such operations they have been small hobby/research type things and involved post de-lidding cleanup and much larger feature sizes than are common today. Perhaps large operations have developed solid processes for this, but I think most of their effort is getting it right the first time. Only the reverse engineering and other spy types really do a lot of this.