Currently, some of our relationships were created with the "Create an intermediary post type" checkbox checked on, even though those relationships didn't require them. So we are left with many orphaned empty pages being populated on the front-end for each relationship. Is there a way to delete these without deleting any of the relationships?
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To delete the leftover intermediary posts:
You should try to navigate to:
Toolset => Dashboard
- On this page on top right corner click on "Help" button
- Further click on "Toolset Debug" tab and click on the link "Toolset Debug Information and Troubleshooting ."
- On Troubleshooting page - you will see a section "Delete leftover intermediary posts", within this section you should click on the button "Delete leftover posts"
So just to clarify, these are not "left-over" intermediate posts, the relationships I have set-up are still in force, and necessary. I just don't need the intermediate posts, and I believe the setting to have intermediate posts for that relationship were set up by mistake. If I go through this process, will it get rid of these intermediate posts, even though they're still connected to relationships? Will it delete the relationships as well?
When you will have many-to-many post relationship the intermediary post type sits between the two post type to form many to many post relationship.
Having said that - The intermediary post type single post item holds the information that shows that the post X of post type "ABC" is is connected connected with post Y of post type "PQR". If you have intermediary post type custom fields that that information also be available with this single item in addition. So, this intermediary post type is required actually to form many to many post relationship.
If you want to hide the intermediary post type displaying from the backend you should just edit your post relationship and uncheck the checkbox setting "Intermediary Post Type visible in WordPress admin menu." from your edit many-to-many post relationship page.
I'm less worried with these posts appearing on the back-end, and more so worried about blank pages generated from the intermediate posts appearing on the front-end, and in Google's search index.