This extension to the already answered question Do ADA Refactor/JARVIS Virus count as a portal capture for missions? that states that flipping a portal to your own faction counts as a capture or upgrade of the portal.
There are cases where a portal is already owned by your faction and maxed out such that an portal upgrade is impossible. Does flipping the portal via ADA Refactor or JARVIS Virus to the enemy's faction count as having captured the portal since it will be under your codename?
No.
If you flip a portal to your opponent faction, it will be owned by _JARVIS_ (if you are Resistance and flipped it to Enlightened) or _ADA_ (if you are Enlightened and flipped it to Resistance).
However, once you flip it to your opponent faction, you can then capture it and that capture will count towards your mission objectives. You can wait an hour (the flip card cooldown) and use a flip card to flip it back, or smash it and rebuild it "manually".
Please note: Flipping friendly portals, especially ones fully deployed and L8, is generally frowned upon, especially when done for personal gain.
Does flipping the portal via ADA Refactor or JARIS Virus to the enemy's faction count as having captured the portal since it will be under your codename?
It will not be under your codename, it will be under _ADA_ or _JARVIS_, so it will not count as capture. On the other hand you now have a chance to take the portal down and capture it the regular way.
