The problem was encountered when we have deleted the existing repository with audits because we wanted to include not just the trunk but all its branches. The thing was that the deleted repository in Diffusion was not the first one to be imported again.

So after deactivating Spaces, users cannot see "Repositories" and "Tasks" again. I have tried logging in another administrator user but it still cannot see all repositories and Tasks..

I am currently evaluating Phabricator for use in our company. The one I have set-up is for evaluation purposes only.
I have created an additional task only so that I could send it as a screenshot here. That's why it only has me on the subscribers and authors filters. But the issue was that I cannot see repositories and Tasks in the "All" filters that I have created.
I cannot remember what I have done in the config that brought to this. I have just restored Phabricator to a previous snapshot.
Thank you for the support though! I appreciate it!