kraemoloblog

Ran into a few issues when combining all of the duplicate instances that comprised the CrateA mesh and had to do the following:

1. Make each instanced mesh unique via the MakeSingleUser (object+data) function
2. Ensure all of the UV maps from each mesh that would be joined together were the same. Apparently, Blender defaults to giving unique objects unique UV map names, which can cause the previously packed UVs to get unpacked and/or potentially in need of complete UVing all over again...though I can't speak to the latter part as I didn't look into it. 
3. Clear the custom split normal data on certain objects. Again, I don't know why this would be necessary, but prior to doing this I was seeing previously flat shaded corners areas become smooth...as if they were completely ignoring the autosmooth (30º) despite it being enabled. 

I suppose the lesson here is that each mesh contains a bunch of its own data that must be taken into account when joining objects together. I expect I'll be running into this a lot as join is a common function.