Flatline overwrites any effects that set a creature's power and toughness
For regular upgrades I highly recommend: Vito, Thorn of the Dusk Rose, Mondrak, Glory Dominus, Anointed Procession, Parallel Lives, Eerie Ultimatum, and you can also run the Cat Oven combo with Cauldron Familiar + Witch's Oven + Clock of Omens, and there's the Ballista Combo Heliod, Sun-Crowned + Walking Ballista, and finally the Exquisite Blood Combo since the deck already runs the other piece Sanguine Bond One Down, Three to Go
I spoke to Dave Chalker, an extraordinary game designer with deep expertise in both chocolate and peanut butter (I think D&D is the chocolate I forgot to ask Dave)
So to be safe, it's always a good idea to read up on and play the weekly events when there are good looking rewards on the line -- besides, almost every event gives out a good amount of gems (see the monthly gem reports, e.g