Code:
This hasn't happened to me so far. Can you post an example ePub file that demonstrates this?
We made a ePub2 in 2014 with a SVG cover with Xlink:hyperlinks (click on title jump to beginning, click on Author jump to Bio info, click on publisher logo jump to colofone). We made a pdf version and a ePub, using Sigil to split the file. Well, after the Sigil splitting the SVG code was destroyed.