Direct from the factory, the entire reel is sealed with a desiccant in an air-tight package. The piece you get from your vendor was cut after the reel was opened (i.e. no further moisture protection). The hole in the back of the small piece you received allows the desiccant to absorb moisture as a drop in temperature might increase relative humidity in the sealed reel during shipping. Less than 10% relative humidity in the mid 60°'s F is equivalent to 100% @ 33°F. The royal blue emitter might be able to withstand tremendous heat from soldering. But we are talking about the bond of its fluorescent phosphor coating. It's not necessarily a snafu on SSC's part. It's just the nature of the bond between the phosphor and the emitter.
Sorry to say it sounds more likely that brown only when turned on might be the effect of delamination from too much heat while soldering. Here's another excerpt from W724C0.pdf:
2. Hand Soldering conditions
Lead : Not more than 3 seconds @MAX280
Slug : Use a thermal-adhesives
Does a 60 watt iron only heat to 536° F? You did say you had some "trouble" while soldering. Was that more than 3 seconds worth of trouble? Is it too late to say I hope I'm wrong? Remember this is all pure speculation on my part.
FWIW, the first LED mod I did was a Fenix P2D that originally had a P4 emitter. I put in a WC tint Q5 binned emitter I bought from Cutter. It was in the mail for a lot longer than a week. I read in a comparable Cree pdf the same moisture waning AFTER my mod. A simple PCX lens used to project the LED's die structure on the wall revealed yellow spots in each of the 9 dies. I always wondered if I damaged it from soldering.
I used a 150 watt Weller gun if it makes you feel any better. I'm sure it didn't stop at 280°C either. We use the same type of ceramic boards that Cree uses on my job. A small screwdriver used to burnish the surface of the contacts and tremendous heat very fast works best. Flow soldering is different because you heat up the whole piece. In fact after several seconds of less heat while hand soldering, it is possible to melt the entire land away. I didn't take any pictures, but I got nice shinny balls from my 150 watt Weller in less than half a second. That's balls largest at the base, so not cold.
Here's an idea, if a little too late to be of use to you. After I Arctic Silver epoxied my P7 onto its MagLite D cell heat sink, I warmed it up with clip leads hooked up to the batteries until it was too hot to handle, before I soldered the leads. Too hot to handle is only 55°C and they say it only needs to be baked to 60°C.