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I am working in a multisite network and I saw that I had CPT UI network activated, so I wanted to turn off network activate since only one site in the network had CPT UI generated posts. I upgraded to 5.9 then deactivated network active and reactivated only on the one site in the network. I tested a CTP UI post and the post URL 404’d.
I went back and did the same BEFORE upgrading to 5.9 and the CPT UI post URLs were fine. Then I updated to 5.9 and tested and they were still fine.
So, it’s something in the deactivate all sites and reactive a single site AFTER upgrading to 5.9 that caused the links for the posts to 404.
You may want to check into this. Thought I’d leave a message to let you know of my findings.