Yes. Normally each patch will need to be reapplied. To quote myself:
3) Future updates should not be affected, but infact, will likely replace your large address aware executable. We should try future updates without this workaround to see if CA fixes the issue somehow. But don't be surprised if the crash issue comes back after updates because the exe has been reset to not being large address aware. Then you will need to make the new exe large address aware again and use it. Don't use the previous altered exe after updates.
If you tried to reuse the old altered empire.exe and now no longer have the brand new patched one anymore. Then delete the empire.exe in your game folder and use the steam feature to verify file cache and that should re-download the latest empire.exe from steam.