Okay so. Elminster has explained to me basically what PNAMs do. They aren't really visible in GECK but you can see them in FO3edit.

You know how you can have a dialogue topic, a single topic, but have multiple things in there? Like, you can have one topic named "Oh, go to hell!" but, it can be the response like for like 10 different NPCs, and each one has a distinct reply, and then at the bottom there is a generic one that catches stuff if for some reason an NPC that SHOULD have a reply in there kinda doesn't? Apparently, each of those single responses has a PNAM record, telling it which response lives above it, and which is below it, in that whole topic.

Well I first noticed when I loaded my mod with Broken Steel that Dogmeat's GOODBYE line no longer worked. Your "GOODBYE" prompt on Dogmeat was now "I need to go now", being pulled from the generic entry at the bottom of the topic, and Dogmeat would say "Come back if you need something" instead of his own GOODBYE line, which is barking.

Now, in the latest FOOK merge I'm working with, and with all of the DLC files loaded (I dont know if that has anything to do with it), the GOODBYE lines are trashed throughout the whole GOODBYE followers topic. They are all giving me the generic line.

.... Has anyone dealt with this, and have suggestions on the best way to deal with it and repair it, if it is repairable? I don't quite know what to think.

Can't say anything about PNAMs, but I will say I've had what sounds like this same issue with both the goodbye and greeting lines when I was working on my battle arena dialog a while back. I had forgotten to exclude the whole custom quest, not just the custom topic lines, and so various NPC's throughout the game were dropping into my quest and hitting the generic (non excluded) entries before they hit their own, so their intended replies got beaten to the punch. Fairly easy fix once I tracked it down, but again might not be the same issue.. mine was trying to work too fast.