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Will i do some serious damage by drilling out the hole to make it big enough for the Di2 cable?
Not if you do it carefully, no. You only need a 6mm hole for an e-tube Di2 cable, so the difference is minimal. Provided that there are no frayed carbon strands, and the edges are nice and smooth it should be fine. There's a lot of material in the bottom bracket area, and enlarging the hole slightly won't make an appreciable difference. Bear in mind that if the hole is actually the end of a metal tube (it is on one of my crabbon fibber frames) you need to find a way to remove the tube.
I'd be perfectly happy to do it to one of my frames - one of my winter jobs is to drill some new holes in my Cervelo P2 frame - but YMMV.
I'm moving my Di2 from my BMC frame to my carbon CX frame. The rear derailleur and the brake cables are fully internal w/ nice grommets that allow plenty of room for the Di2 cable.
The front derailleur only has a standard cable hole:
Will i do some serious damage by drilling out the hole to make it big enough for the Di2 cable?