2004 A6 Quattro S-line 2.7t.

So my only key fob went thru the washer and is ruined. So...I had a new key cut, went to a specialist (who rebuilt my instrument cluster). I went with the new key/fob and a second new fob for my first key. He coded the keys in, both work. However he could not code the fobs in using the vagcom OR the manual method of locking door with another key in ignition, pressing unlock button, etc. He gave up and sent me home because he could not figure out how to fix it.

I cannot find anybody that knows wtf to do here. I'm sure the dealer would be happy to help me for $600 but that aint happening. So 2 working keys, 0 working fobs. Would love some help if anyone knows what could be my problem. Web searches came up empty.