Fixing errors related to orphaned section id on articles

I have a journal that we are testing upgrade to 3.X from 2.4.
Everything went smoothly except a DATABASE error was thrown each time we logged in.
The forum her led me to an issue related to the previous articles table with NULL section IDs

So I need to assign them IDs . Before I do that, I need to understand a few things.

This journal has at least 2 overlapping CFPs so they create a section ID for each CFP rather than allow users to upload to generic “Arcticles” section. When an article has been accepted, it is moved to the “Articles” section for that publication by Journal editors. (If there is a better way to do this I would love to know what that would be)

I saw that the orphaned articles were all rejected papers. I asked, but they said they did not DELETE the assigned section. (I have my doubts about this. I don’t see section IDs for each and every Issue they have currently published) But even if they did, I need a solution.

Second and most important problem is this: Authors who have been rejected and who are in this set of articles with NULL sectionID are appearing in the Journal search. Their name, title, and Issue are displayed. When the user clicks on the item, of course they are taken to the issue and in fact they are not in the list of aritcles. But the search engine should not reveal them.

I have tried assigning them any old sectionID not currently in use (fixing the NULL secID problem) but they still appear in the Search engine results for the journal. So I would like to know (Im working with manual changes inside the mysql through phpmyadmin) what other element in the mysql table might be allowing an article that is archived to be indexed. What would be the correct value.

I have suggested to them that we create another section called Unapproved articles (REJ) and when editors have a result, they should either move the accepted articles into section “Articles” for publication, and should then move rejected articles from the Section_issue to this permanent section “REJECTED” before deleting the section that is no longer needed. Would this be the best approach?

Thanks in advance for any suggestions and/or solutions to this problem before we attempt to migrate the journal to version 3.