Unfortunately Flight of the Eisenstein is where HH stops following an easy reading order, I'm about 23 books deep in the series and at least a dozen has had Istvan 3 and 4 either be the opener for a book, happen in the middle, or end on it.
The problem with out right skipping books is that 90% they tie into events from another book, for instance the first assassinorm book is almost completely skippable except one of the minor Luna Wolfs/Sons of Horus captains that has a decent pressions in the first 4 books gets killed in in, so unless you've read it your left scratching your head wondering what happened to him.
So far I have only come across 4 outright skippable books since they don't tie into much
Descent of Angels
Battle for the Abyss
Fallen Angels
The Outcast Dead
The Anthology's are somewhat skippable, some of the shorts are pure fluff others tie into the plot for serval books