As PDFs are no longer common for ordinary eBooks it is only recently that this problem raised its head again. Seems that a decent reflow function is unusual, only my Pocket Book does a decent job of it. Most readers and reader programs just fit the width of a pdf but you have to scroll the vertical overflow page by page instead of just next paging. Funnily enough many years ago had a Cooler that also handled it correctly, wonder if Pocket Books and Coolers share a common heritage...
It also seems that most eBook software falls over on really large Pdfs, say in excess of 50 mb. Kobos and Aldiko can't handle them for example
This partly depends on the software you choose to use for reading the PDFs. Have you visited the KO Reader forum?
Can it handle them? The pdf is 80 mb and no chance on the standard Kobo software. Had koreader for a while but at the time saw no advantage. Impressed that pocket book does and also reflows properly..