You'll have a hole somewhere if you assume everything the books say are true, since they contradict each other. I have yet to find an explanation that can account for all of this :
System Failure, page 26
"Following Acting-President Daviar’s orders, Colloton declares Martial Law."
System Failure, page 106
"President Pro-Tempore Gene Simone will fulfill the duties of the President until President Haeffner and Vice President Daviar have been found. Martial law will remain in effect until the end of this crisis." [speech by General Angela Colloton]
Shadowrun 4th edition, page 34
"Under order from the President prom tem, General Angela Colloton declared martial law until the country was brought back under control.
When elections were held again, we had little choice but to elect a President who ended up being nothing but a tool of the corps during his entire term."
Running Wild, page 73
"Still ostensibly chaired by former UCAS Vice President Nadja Daviar, the [Draco Foundation] publicly works to enhance metahumanity's ability to interact effectively with the Awakened World."
Shadowrun 20th Anniversary, page 35
"Under orders from the President pro tem Nadja Daviar, General Angela Colloton declared martial law until the country was brought back under control."
Corporate Guide, page 49
"Nadja Daviar - Haeffner's vice-president and former voice of Dunkelzahn - went MIA during the UCAS coup d'état in the early days of the Crash 2.0." [comment by Frosty]
Corporate Guide, page 50
"It's only gotten worse since Nadja Daviar dropped off the face of the earth after the Haeffner assassination." [comment by Kay St. Irregular]
"Maybe the foundation decided to take a more active role in what it assumes would be Daviar's best interests." [comment by Plan 9]
"That's assuming that the foundation doesn't know Daviar's whereabouts." [comment by Frosty]
Corporate Guide, page 54
"The Draco Foundation - executor of Dunkelzahn's will - has controlled Gavilan Ventures ever since its CEO and former UCAS Vice-President Nadja Daviar went missing in 2065."
Discarding Running Wild is almost a necessity to make sense of it (remembering RW was originally planned as a 3rd edition book, a sloppy editing may explain some mistake). Also, the person who added Nadja Daviar name in the corebook history seemingly did not know what "president pro tem" stands for in the US. It might worth also noting the last quote from Corporate Guide says Daviar "went missing in 2065", which would be at least two months after the failed coup d'état. Daviar disappearing two times may provide the best explanations.
I would run it the way that 4A was just a typo (that´s the simplest solution and thus also the most likely for me), Daviar became acting president after Haeffner was lost, then vanished herself after an attempted chimera assassination. Gene Simone -freshly elected PPT by which ever members of the senat where still available- took over controll, and made the presidential elections that followed right after the crash, but turned into a corporate puppet. Coloton won the hot seat next.
The DF might or might not know Daviars whereabouts, but they sure got some instructions how to handle Gavilan Ventures, a departure from previous behaviour can mean they ran out of instructions or the situation changed enough to trigger some conditional instructions.
For what Daviar actually does with all that free time, my guess is as good or bad as anyones. I like the idear, that she is still hiding from Chimera, while taking care of undercover or private business. In my game she will certainly not sit her babies with RM, first and foremost because he´s so anoying. Maybe she makes backroom deals with the IEs/GDs/some other crazy guys. Though she may not be an IE herself, I always thought she (and Claudia Romanov) was at least a spike baby, as she apeared out of nowhere before getting picked up by the big lizard. I also thought she would be a Drako herself (either that or latent magic, since DZ never allowed her to have any cyber)- which might also mean that she got snuged away by some GD as a status symbol.