I actually did try LRFtools a while back. While it did save the links correctly, it also would randomly insert like half-sentence spaces for some reason. Couldn't figure out why. For example:
text text text text text text
text text text text text text
text text text text text text
Except that space wouldn't be a full one, just a partial or halfway space.
As for Sigil, I gave that a go too but every HTML input I tested didn't have or generate a stylesheet. So the output would have huge fonts. Isn't there a way to auto-generate a stylesheet for an HTML file? Only could get EPUB input to make the needed stylesheet with all the code intact.
EDIT: Here is a sample screenshot of an LRFTools output EPUB:
Notice towards the bottom of the page where the lines are inserted between sentences? It seems to do that whenever italics are used. I tried in Calibre to do an EPUB to EPUB but the spaces still persisted. I checked in Sigil to see what the stylesheet showed, but I couldn't find anything problematic. Not sure what to do about those italic spaces.
EDIT 2: Wow, duh. Just now notcing that LRFtools also doesn't retain spaces. Just can't catch a break here.