I have a Flanders Brown ready to be kegged for aging, and I'm going at add some oak cubes for the flavor and oxygen and bugs. I've heard it's a good idea to boil the cubes first, but I feel like that will kill off the Brettanomyces that naturally live in them. Is this a valid worry? Does it even matter since I used a Wyeast strain that has all sorts of lambic bugs to begin with (including the beloved Bretts)?
I think relying on the supposed wild bugs in the wood naturally is generally a bad way to go. You've already done it "right" by pitching an appropriate brewing Brett strain you got from wyeast. So go ahead and steam your oak cubes first. You want to give the bugs you put in there on purpose the best chance at being the predominant character in the final beer.
Don't over boil your cubes, you'll just pull out too much of the wood characteristics that you want. I bring water to ~180F and let the cubes sit in there for a bit, then put them in.
Another option would be to put the wood into a steamer and kill any wild yeasts/bacteria/molds using steam. No yeast naturally lives in wood unless the wood has been used previously for brewing/cidermaking/winemaking. All you need to worry about is the surface nasties.
If you don't have a steamer, you can simply put a colander over a pot with a small amount of boiling water in it, and put your wood chips/spirals in that.