Oww, heard the same thing and that was rather painful, so I found this thread!
There were two crazy frequencies in that file, one around 6694hz, lowered that one enough that it was still there for the effect but otherwise not painful, but then noticed a second loud one that was now dominating at 13389hz, fixed that as well. There are still a whole lot of high frequencies, which is not at all pleasant for my ears (I want to pass out the higher frequencies pretty hard, but that would understandable get rid of a large aspect of the sound), but it's probably sufficient now. The altered file is available at: https://overminddl1.com/Factorio/RFP/reactor-running-edited-1.ogg
The particle-accelerator.ogg could use a bit of massaging as well but it's not quite to the level of painful, just uncomfortable, like the above edited reactor one is now as well.
