So you're asking two similar questions here; 1st, how do you handle acquiring a Skill you already have during CharGen? 2nd, how do you handle it after CharGen?
How you thematically handle purchasing new Skills after Character Generation and during gameplay is up to you, but the mechanics of it are explicitly enumerated from Page 74 of the Black Crusade Core Rulebook through until Page 81. Specifically on Page 77 under Skill Advances:
Characters learn new Skills or improve existing Skills by selecting Skill advances. As with characteristic advances, the cost in xp of a Skill advance is affected by the path of their devotion(?). This represents Heretics following certain paths taking more interest in learning Skills that pertain to their path, rather than non-related Skills. Skill advances are divided into four progression levels. These are as follows:
Known = no penalty to Skill use test
Trained = +10 bonus to Skill use tests
Experienced = +20 bonus to Skill use tests
Veteran = +30 bonus to Skill use tests
So in reality, you never acquire a Skill you already have – you simply purchase the next level of training in that Skill, which will always cost more than just learning the Skill for the first time (purchasing Known-level). Like with characteristic advancements, you can only buy each level once, which then unlocks the next level. It’s built to be a natural progression with generally diminishing returns. You can see what I mean with regards to Skill/XP costs in Table 2-7 on Page 77.
Here's four different options that came to mind immediately, ordered by which I personally advocate for the most.
- Skills stack, start with +10 (Trained) level of Skill // EX: extra Common Lore (A) becomes Common Lore (A)+10
I feel like this most accurately depicts the effects of having a Skill doubled up, and the mechanical bonus it gives reinforces the idea of the character having had so much experience in this one field that they get the bonus.
- Pick a new, similar Skill only // EX: extra Common Lore (A) becomes Common Lore (B)
This choice feels like it fits the theme of a character that knows a boatload of lore. Most characters don’t start with much in the way of Lore, so if you were (un)lucky enough to have two of the same, it helps everyone to be able to pick another one instead.
- Reverse-convert Skill to XP // EX: extra Common Lore (A) becomes experience points
This allows the most Player freedom, but results in the potential for abuse, because it allows you to grab an important Skill like Dodge that you might not otherwise have. All you would have to do is determine the cost of buying the Skill and give it to the Player as XP.
- Repeated Skill is redundant, no change // EX: extra Common Lore (A) disappears
The best I can say about this option is that it’s an option. I don’t think it’s particularly fair or fun, though.