All right, Accordance is working speedily again and I have discovered the issue - it is definitely a dropbox sync issue.
WHAT I DISCOVERED
When I finally got time to explore why my Accordance install was slowing down and becoming unstable on my macbook I noticed something interesting. First, when I went to open user notes I was offered a selection of hundreds of files, even though there was only my notes and a "conflicted copy" in my accordance files folder. A conflicted copy is how Dropbox identifies when a document was opened simultaneously on separate devices and then tries to sync. It probably was created when I had both my Mac Accordance and iOS Accordance installs opened and synced through dropbox on my iPad or iPhone while the Mac version was simultaneiously trying to sync. This is not a big deal, it happens all the time.
For whatever reason, the Mac version of Accordance kept adding entries for that "conflicted copy" notes file in the "User Notes" file in ~/Library/Preferences/Accordance Preferences. When I opened the file in Text Wrangler, it's ends up being 984 lines (and this was causing my "add parallel" click to take 20 seconds to open). The sheer number of entries for this one file was slowing it down.
It's also why, when I renamed my notes files, I thought I was stuck in an "this file is no longer available loop" - I would have had to click the button 984 times to work through every entry in the file! Actually, it' would have been twice that, as my sample notes also had a conflicted copy.
So, I renamed that preference file - which erased the speed issues. Sadly, my notes file was no longer associated with Accordance. So I renamed my old files, deleted all the "conflicted copies" and did a local wifi sync with my iPad - everything is back to normal.
So, there IS a sync issue with dropbox that apparently has a very narrow trigger that I just happened to trip. A temporary fix would be to tell Accordance to not allow for duplicate entries of the same file in it's preferences - why it was assuming this was a new file each time must be how the user Accordance files are reading the conflicted copy dropbox metadata. The name is the same but each sync changes something in the metadata which makes Accordance think it's brand new.
Since I know how to fix this, I'm going to re-enable Dropbox sync to see if the issue re-occurs.