I think I fixed my issue.
I exported the design to an ASCII file, opened the ASCII file in Notepad, and searched for the name of the object reported in the database integrity test.
After I found the name of the object, I deleted only the name, and saved the file.
Then, I opened a new startup file, imported the ASCII file and everything works now.
I was able to regen my apertures cleanly.
We'll see how it plots.