For this build, you could replace Flow with Shield of Shadows if you're not too concerned about running low on energy, and would prefer a little bit more durability. When I used this build without Flow, the only times Desecrate turned off were when I wasn't running around picking up energy orbs. Otherwise, it's pretty effective with his base energy pool, especially with Nekros Prime's increased base energy pool.
I have not had it turn off due to running out of health. As long as you're near a death, for Nekros' passive heal, combined with Rejuvenation and the health orbs, you shouldn't ever be in a situation where you're worried about low health. This build leaves all your energy for whatever you want to do with his other abilities. Shadows of the Dead won't last long, but are still handy in a hairy situation, and when they expire, Desecrate gives you health orbs from them. Optionally, substitute Shield of Shadows for Fleeting Expertise. This results in an increased cost of abilities, but the Shadows of the Dead will last longer, and provide some durability in harder missions.