The Overseer ability is an instant hull boost, and can be done continuously if there are enough of them....it is not uncommon for the AI to have lots of Overseers, and when you focus on a single ship, you can bet every single one of those overseers is going to be adding HP as fast as it can to the target you're hitting...getting a boost of 250 HP every second or so can make it difficult to take out any target...given that the shields were regenerated as well, its clear that the Ultimate ability, disintegration, was being used...however, the Overseers + Repair cloud would have made it extremely difficult to take out that ship until the overseers and skirantra got low on antimatter...
In general, its likely you'll never need more than 4 capital ships unless the game goes on A LONG time....to put things into perspective, one capital ship at lvl 1 does about 50 damage per second...5 Kodiaks (which is 50 fleet supply, the same as a capital ship) do 18 * 5 = 90 damage per second...capital ships don't dish out that much firepower until their higher levels...abilities are what make capital ships valuable, not their firepower...you are better off having 2 or 3 high level capital ships than 6 low level capital ships, and with fewer capital ships, they will level up faster since experience points are distributed amongst all capital ships in the gravity well..