I sample mine at the 6 month mark and then every 3 months after. I would use a wine thief, but I don't have one. Instead I use my auto-siphon that has been designated to the sour side. I fill just enough to take a hydrometer reading, which is 4 oz.
I try not to destroy the pellicle, but it happens once in a while. I don't think the added oxygen every 3 months is going to ruin the beer. Plus I also take this time to add more maltodextrin, fruit or fresh wort to feed the bugs depending on what I think the beer needs. This produces some CO2 and will fill the head space pretty quickly.