There are multiple cases here.
Let's say you have the following projects in your JIRA instance: P1, P2, P3
And you are seing all 3 in Portfolio but want to exclude P3.
If all your Boards JQL look like: PROJECT IN (P1, P2)
-> Then P3 should not show, and I'd advise contacting the support if they do show
if one or more of your Boards JQL does not include any project limitation (e.g. Label = 'A' OR Project = P1) then I'd advise updating those JQL query to exclude unwanted projects explicitly: Project != P3 AND (Label = 'A' OR Project = P1)
This should ensure we are not trying to include issues from unwanted projects.
If you feel the list of excluded project is getting too long, maybe the list of included project is shorter.
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