For this question, let us suppose that we start with a 15th level character who is a 7th level Dragon Disciple with a base intelligence score of 10, increased to 12 by a Headband of Vast Intelligence +2 (with Knowledge (Arcana) as the associated skill). His feats include Celestial Obedience, with Shei (from Chronicles of the Righteous) as his patron deity.
At this point, it is easy to calculate how many skill ranks he gets -- we treat him as having an intelligence score of 10 and then assign him 15 ranks in Knowledge (Arcana). So far, so good.
But now let's have this character gain another level. As a 16th level character, he gains an ability score increase -- let's apply it to intelligence. The second boon from Shei kicks in, aging him mentally to middle age and thus giving him another +1 to intelligence. He takes 8th level as a Dragon Disciple, giving him another +2 to intelligence, for a grand total intelligence score of 16.
However, this newly gained intelligence is easily lost. Removing his magical headband not only costs him his +2 enhancement bonus to intelligence but in this case leaves him with insufficient ranks in Knowledge (Arcana) to qualify for the Dragon Disciple prestige class -- so that +2 boost to intelligence from his Dragon Disciple levels is also lost. Finally, he fails to perform his obedience, reducing his intelligence back to 11.
Which finally brings us to my question. This character has just attained 16th level. He is wearing his magic headband at all times and faithfully performing his obedience every day. For the purpose of calculating how many skill ranks he gains, what intelligence score should we use? Would the correct answer be 14 (excluding only the enhancement bonus from his headband) or some lesser value?
The correct answer is 16, but he does not get skill points for the two points of Intelligence he gains from the headband, or rather, the skill point for those points of Intelligence is the Knowledge (Arcana) point associated with the headband itself, and so the headband comes with a bonus skill point that has already been assigned.
The problem is once you remove the headband and no longer have the requirements for the prestige class you don’t get any of the benefits from it. This could mean you lose access to all class features. Does this include skill levels? Most classes that you can fall from have some sort of ex-section that spells out what you keep. Dragon disciple does not have this so who know what you actually keep. As a GM I would not allow the skill points from the headband to be used to qualify for a class. A feat yes, but not a class.