Complex sentence: It was fortunate that after the propulsion stopped due to the flooding, "Endurance" drifted over an area shallow enough for anchors to hold and stabilise her, otherwise "Endurance" would probably have been lost by flooding or running ashore.
Split into simpler sentences: It was fortunate that, once without propulsion, "Endurance" drifted over an area shallow enough for anchors to hold. Otherwise, "Endurance" would probably have been lost by flooding or running ashore.