I've noticed that converting certain types of files (I'm looking at you, LRF) in Calibre with the font scaling disabled doesn't always work. What I do for a quick fix is to enable font scaling, but change the base font size to something like 17pt or 20pt instead of the default 12pt. The scaling still won't work, but it'll give you nice fat bold print in a readable size after conversion to EPUB and uploading to your Kobo.
Disclaimer: I'm using the Ubuntu Linux flavour of Calibre, I don't know if this works with other platforms.
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