@ninja:
take a look at this thread:
https://www.mobileread.com/forums/showthread.php?t=83209
Someone created a tool that you can use to (temporarily) fix your ePubs for the Kobo. It parses the CSS and removes the font-size: lines causing problems (or you can set it to delete the css entirely).
The author released a bulk processing version, so in the very least, it should save you some time in manually deleting the CSS. I'd suggest you try it out without deleting the CSS entirely first, since you can preserve much of the formatting this way while still having font-scaling.