Are you sure it was not the extention cable you used to connect the fan an not the actual fan cable ?. I ask as I had a Supermicro chassis that had two rear fans and had to get a fan Y-cable so I could power both of them. I got one from Amazon, connected it and got a nice puff of black smoke come flying out of the back of the server with a stong plastic burning smell. The problem was that the Y-cable was not rated for 12v fans and acted like a fuse and glowed, melted its plastic sleave (smoke and smell) and then melted itself. On getting a better quality cable I had no more issues.
The green shroud for these fans can be a pain to get off especially around the wires but the part that holds the plug just unclips (you have to get the angel right) and then I just use some snips to cut the frame where the cable needs to pass to take the fan out and snip of the clips holding the actual fan in the shroud and slide it out.
I have done a couple more quiet fan kits with units I have sold and once you get the hang of it, it is quite easy to take them out safely. I will see about taking some pictures next time.
My soldering has improved quite a lot as well now I have worked out an easy techneque for that as well
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RB