If you run into this issue again, please add a comment with the details about the search here. Then I will try to debug it.
Also thanks for reporting it so far.

To debug search could you provide me with a specific search string you used with the form, the first few results it returned and some results you expected to show up (for example by searching on a Lemmy instance and linking to the threads)?

Comments not properly federating

Do you mean federating in or out? Or is it just the notifications which appear late (we currently have problems with the notification processing)?

searches for topics recently mentioned on other instances not showing up, despite not being defederated

Can you give an example search and what you expect to be returned so that we can check what is happening?