I tested deleting a section on our test site that is running 2.3.8. I created a section, submitted an article to that section, published the article to the current issue, and then rejected and archived that article. It does not appear in the current TOC any longer after rejecting and archiving the article. I then deleted the section in the Journal Sections portion of the Journal without receiving any error.
I also created a section and submitted a second article to that section. Without publishing the article, I then logged into the Journal Management pages to delete that section. I did not receive an error while performing this action either, and the submitted article had automatically been switched to the default Articles section while in the Editing queue.
I also submitted an article with a specific journal section, published it, and then deleted the section while the article remained published. I also did not receive an error message while doing so, and the article record in the published archives automatically switched to the default Articles.
I don't have a test installation with the version you are running, so upgrading your installation might solve this problem. I'm sorry that I don't have another solution, but I wasn't able to replicate the problem on our test installation.