OK ... some interesting peculiarities have been found. It did have to do with the naming of areas, but not due to copying them or exporting them into a hak and removing from the module. It has to due with the fact that some of the newer areas I was trying to add to my serverside hak were using a color/alt code prefix to colorize their names IG. I've been using a color code prefix to have my area names display in yellow as I've been updating them the past 6 months. This moves them to the top of my area lists both IG and the toolset which is handy in the toolset especially to see which I still need to finalize (was updating loot and foraging module wide) and lets players no not to bug report non-updated maps.
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Exporting and adding these areas into my serverside hak however would break their transitions and, if I tried to do a module build from the toolset, it corrupted the whole module each time. Removing the color/alt code prefixes and re-exporting them all and then deleting them from the running copy after adding to the hak fixes the issue now.
Long story - short, don't use color code prefixes in anything you want added into a hak.