I work on Multibody parts a lot, almost exclusively with no external references, and we do not use EPDM. I always make sure to have a clean tree with not failing features or even yellow warnings. The part will rebuild fine during the day and I am able to save it. Often time when I come back to it later (re-open) Solidworks will immediately rebuild the entire tree from the top before I can do anything (even something as simple as rolling back 1 feature). First off, why does solidworks rebuild right away (it takes time), and second why do features often fail at this point (even though they were previously OK)?
Sometimes is refuses to find certain faces of a surface knit, or other times, edges get missed from a fillet, or even a converted edge in a sketch might no longer be found. All of the items are easily fixed by a quick edit (if I remember which they are referring to). Sometimes it is as easy as that, but other times it is a slow process to fix dozens of features out of my few hundred.