I bought the Neverwinter 2 edition with 1 add-on. Can I add my own add-on to the file?

Not sure what you mean here, GoG version comes will all three official add-ons.

Did you meant that you already own the game with one add-on and would have liked to only buy the remaining Add-on on GoG ? If that's what you meant then, no, it's not possible GoG only sell the complete version not the add-ons separately.

I bought Neverwinter Nights 2 with one add-on. It did not come with the additional add-on for the game. If I purchase the game from a eBay can I add this to the GOG version

GOG's version should include all 3 expansions. Are you sure it only has one?

If you bought NWN2 on GOG, it has all 3 addons.
from the game card:
"Neverwinter Nights 2: Complete includes the original game, and three expansions: Mask of the Betrayer, Storm of Zehir, and Mysteries of Westgate."

No you cannot add retail games to GoG, at least not yet.

True, but he is not asking this. He is asking if he can use a retail cd with an existing GOG game installation, not redeem his physical disk.
A better example would be if Deeper Dungeons (physical form) can be installed over GOG's Dungeon Keeper, since DK from GOG is currently missing the expansion.
Since NWN2 though should contain all 3 expansions, the question is moot.

That's what I thought too (in my first post), but now I not so sure.

Therein lies his problem. He's convinced he didn't get the add-ons/expansions when he bought it. Anything is possible I suppose, but I seriously doubt it.