When you are defeated in an MMORTS battle, you do have some things to help you catch up...
The main advantage you have is hundreds of bodies to loot. This won't recover your losses, but it'll help.
Also, buildings do not die. They go to very low HP, are unable to operate, and wait for repair (although elven great tree-buildings work a bit differently).
Lastly, you do not have to kill every enemy unit to win a battle sieging someone else's homeland.
I think you have not understood/found the thread that explains this. Once you loose you revert back to your city/empire two log ins ago.
This system was a very old idea..Before our game was planned to be an MMORTS. The game concept used to just be a regular RTS, with your city saved through each match.