Presta to Schrader Conversion
Regarding original question: I have personally drilled out approximately 6 wheelsetsto convert them from prestato schrader valves. I have not yet had any of these rims break even though I use them to drive down flights of stairs and such. Mind you I am a lighter rider (approx 80kg), these (aluminum) rims were used on hardtail mountainbikes. Make sure to debur(remove sharp edges from ) the drilled hole properly.

To try and decrease the amount of flats you get you could do a few things:

-make sure the rim tape is in good condition (no tears/holes, make sure it's properly aligned in the rim)

-remove rim tape and check if any spokes protrude more than approx 1-2mm past the top of the spoke nipples, if they do consider shortening these spokes with a file, dremel or the like or adjusting the spokes such that they are no longer protruding (if possible whilst keeping the wheel true/round)

-check rim bed/edges (where the tire contacts the rim) for damage (sharp/pointy spots which could potentially damage the tire), if you find any sand/file them down so they're smooth

-check your tire for pieces of metal/glass/other objects embedded in/under the surface (by rotating the tire whilst removed from the wheel and pinching it every 2cm approx to reveal any splinters, do this on both the inside and outside of the tire

-check if valve hole has any sharp edges

-whilst installing inner tube make sure it is not pinched in between rim and outer tube (inflate inner tube just a bit, check if it is not pinched anywhere and if all is good inflate the rest of the way)

For fixing flats I personally find it useful to clamp the inner tube with patch in between a bench vice (potentially with some pieces of wood in between the vice and the tube/patch for wider inner tubes), you could also use screw clamps for this purpose.

If you're a heavier rider you might want to refrain from drilling the hole larger but as mentioned I have had no issues with it so far and have been using the 'converted' wheels for considerable time now.