1. IDK what they were told and why they had an illusion he might get the citizenship, but those sudden withdraws without any explanations suggest they are passing the message of "screw you". Normally people people who are on good terms with their "bosses" are less middle-finger-upon-quitting.
2. By the time they withdrew Israel hasn't yet secured the team event spot, so they've done it fully aware this step might cost.
3. Israel didn't give out the GP spots, suggesting papa Borya was under impression T/T would show up eventually, which they didn't, and no explanation was given either.
All that sounds to me like there's some bad blood between T/T and the federation. I am not aware of any issue that might have caused that apart from the citizenship issue, so my assumption for now that they felt cheated giving Israel the spots in the ice-dancing and the team event, and then being denied the ticket to the Olympics. Given that people in the federation knew well ahead Tkachenko is unlikely to obtain the citizenship (I heard it from two sources 2 seasons ago already), and yet T/T seemingly weren't aware of it, I would think the source of their illusion came from the federation in whatever form.
I wonder whether they have prepared the programs and trained for the season, and whether they will show up for the Europeans/Worlds if they did. If they did, then it sounds rather silly to throw away all the investment, even if they don't want to have anything with the Israeli Fed; and if they didn't, then their withdrawal should have been known in the summer already, and then it's even more baffling why no one has cleared the GP spots.