Hmmm... if the new metric screw is stainless steel its probably non-magnetic... in which case it could be right in there but your magnet would fish up nothing. If it was me, my next steps would be:
1. Use a mirror plus a very bright flashlight to inspect inside the best you possibly can. If you're lucky its there and you can reach it with a needlenose plier. Even better than a needlenose for these situations is a large or medium hemostat (I am never without mine)... a hemostat is basically a physician's version of needlenose pliers, only much narrower, much more precise, and it locks. You can prolly pick one up at any farm supply or animal supply store.
2. Triple-check throughout the nooks and crannies of the engine compartment with a bright flashlight and from many angles, cause boy are you gonna be PO'd if you pull off the pump only to find that screw laying on top of the starter!
Good luck... we've all been there (or somewhere similar) and are rootin' for ya.