If handbrake is messing up the fonts, I'm assuming the soft subs are in .ssa/.ass formatting. An option would be to extract these files with MKVextract, use Aegisub to convert the fonts in the file to an installed font on your computer, then use MKVtoolsnix to remux the new subtitles into the original file. It sounds a little tedious, but it only takes a few minutes for each file.
That sounds like what I want to do apart from that I want to keep the font... I actually reallylike it lol. Could you detail that a bit more step by step? Very interested if it only takes a few minutes.
I would prefer a 1 step procedure. Sedulous my problem is the fonts are getting a few errors on letters p,g,y.