Thank you so much for your help. After your comments, I've done some research and noticed that a bug was logged yesterday for chat with refinedwiki theme. Here is the link:
I am only evaluating the theme at the moment but if this is not resolved, I think we will need to select another plugin.
As long the "Allow All" check box under the Chat Access is marked, you should be able to see the chat icon in all spaces:
Confluence Admin > Chat Configuration (in the left panel):
If that check box is not marked then, click on Confluence Admin "Chat Space Setting" and validate if you did not marked any restrictions to specific groups on those spaces that aren't showing the popup.
Yes, I am using RefinedWiki theme and I have customised the space layout on all of my spaces. So that is probably why the chat is working under the profile dashboard as that has not been customised. If I use the admin account, I get the same behaviour as my users. What can I do to try to get the chat link back?
That depends, if removing the customizations solve the problem you would need to adjust your customizations, now if the problems lies on the redefined wiki you would need to send they a email asking for some advise on how to proceed. It's kind of a pain when you get that kind of problem since it's a grey zone on who you should reach for help :(.
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