Vex High Strength Shaft is too thick for holes in the C Channel (or instance). Is it allowed to increase the hole size in the structure for the thicker shafts? Are there different structures like C Channel which have holes to accommodate the thicker shafts? Is it ok to file of parts of Structural elements?
Increase hole size, yes. Are there parts with wider holes, no. Filing, yes, please do so there are no sharp edges on cuts. See <R16> in the Robot section of the rules for information on legal modifications to parts.
You are allowed to modify any non-electronics in VEX, as long as it’s not melted as well as there is no sharp edges as what @John TYler said. If you are doing High Strength, the bearing flats have a LOT of friction on them. I’d strongly suggest drilling a larger hole into the HS hole of the HS bearing flats by around 1-2 milimeters. In terms of drilling into the C-Channels, drill a hole around 3-4 milimeters wider than the hole of the HS bearing flats to prevent metal-on-metal rubbing.