Some more talking to myself here:
I've noticed sometimes quest files with a ~ after the end of the name that are hidden files on Debian Linux. I'm assuming its a way for Debian Linux to back up old version of edited and/or renamed files? I've seen in log that the emu gets confused sometimes on those files. I usually have to "show hidden" files then delete them. Not sure if this was causing the link dead problems, or some other crazy edits. I don't see any errors in the quest logs.
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