Thanks to PUKI on Order for this!
Go to your bugged plot and double click on each structure you want to work with. The normal info window for that structure will pop up. Open your plot window and you will notice those structures are now listed, Unfinished structures you double clicked on should also now be displayed in the Construction Tab.
The buy, sell, and destroy buttons will be greyed out still, however. Flip over to the Permissions tab, and then back to the Plot Info tab and those buttons should now be available. You will need to do the tab flipping trick each time you close and reopen your plot window (you won't have to reclick on the structures).
I was not able to use this trick on a Large Dwarven House. Double-clicking brings up the inventory instead of an info window, so I am not sur how to "force" the structure list to update for these. I have not tried this on silos or other storage, so can't confirm that those also have this issue.
*EDIT* I have now tried it on silos and guild halls, neither of which can be updated this way. Will try and see if there is another way to bring up the info window for these structures aside from accessing from the plot structure list.
The tab flipping trick to get the buy/sell buttons may be enough for some as you can then sell to another character, which has been reported to fix the problem entirely.
Drev