I have Brazillian Cherry hardwood floors in my new home (10 months old) and they have calcium carbonate (also called silica sap) all over them. The builder, installer and independent floor assessor tells me this is the worse case they have ever seen- it looks like someone spilled bleach on about 90 or so floor boards. The manufacturer is denying the boards are defective but is sending the installer 2 boxes of floor boards that they can replace at their cost. My question is this: I am concerned about replacing so many floating boards with glued down boards. Every time I speak with the installer they give me a new story- first, they say, it is bad to replace boards period...next they say it is okay to replace boards but you may have to take boards to the wall around corners so their aren't problems with "fixed"/glued boards around corners...now they are only replacing 65 boards and there is no warranty/guarantee on installation. I am frusterated and in the dark about what to do next. Can anyone give me feedback on the issues that may arise with replacing so many floating boards with glued boards? I feel like I've spent a ton of money on a less than quality product and am being given a less than ideal solution.

The blotchiness you are seeing is not really considered a defect, nor does it always occur. You are unfortunately the owner of a floor with more than usual amounts. I would minimize the number of board replacements to just the most obvious pieces and ones that are not covered by furniture or area rugs.
There is a "point of no return" on board replacement, and since your floor is designed to function as an integrated unit, the more boards you replace, the more potential for problems. This is not to say you WILL have problems, but in essence you are playing a game of "Russian Roulette" with every board.
Over the years, we have had to replace literally hundreds of boards within floating installs and with high success, but not complete. Sometimes, especially with a square edged product, a microscopic outline can be evident around the edges of the board. Also, in areas of high humidity fluctuations, the replacement board can shift loose from the system.
All in all, I would say that you should minimize the replacement boards, and accept the discretion of your installers as to which ones.
In closing this small piece of advice, may I say that I hate "Exotic" woods for a variety of reasons, only one of which is this chemical exuding from within the Jatoba. The problem in our industry is that it is reactive instead of proactive. The marketing people convince the public that this is what they want, and we are left to try and provide it, not always with full understanding of the pitfalls.

I cannot thank you enough for your feedback. I agree, we got a bad batch of wood. No consolation given the amount of money we spent. I also have to agree that the industry does not do a good job advising consumers about potential issues with exotics. We will follow your advice and move forward. Thanks!