I had this issue too. All of a sudden I noted reply link was gone. Another symptom is that comments_number() is always using the ‘0 comments parameter’, even the post having comments on it.
Comment form was down there, there were comments that allowed (should) nested comments on them, but reply link was not there.
A few days ago I updated some plugins, I’ve also noted that for some reason now my site keeps loading and never stops: it’s because some js I can’t identify is not finishing running.
I even thouht the previous js issue was being caused by my theme js, because I’ve been working a lot on it. But now with these comments strange behavior, I decited to roll back my development environment to a point before I updated my theme and plugins… it both loading and comments issue were gone!
Then I went to update my theme, just to confirm they’d come back and start trying previous versions until I’d find the exact version that had broken everything… but no issue was there, comments are being reported, reply link is in its place, and comments_number() is working!
Now I think it may be 2 causes: something in database or an updated plugin. For now I’ll just backup CounterizeII and posts tables and roll everything else back. Then I restart updating my theme (directly to a much stabler version 😀 ) and slowly update plugins.
I enabled the threaded commenting option in the Admin panel and it does not work. Now I’m thinking I have a theme that doesn’t support it. Can I find the code to update one of the theme files? I’m not afraid to do that if it’s possible.
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