All the issues in Jira have to be inside a project, but you can move issues from project A to project B. Here is some documentation to help you with this https://confluence.atlassian.com/jirasoftwarecloud/moving-an-issue-902499026.html
My suggestion is to create a project to aggregate all the issues that haven't any project and when the project is create move them to the right project.
Best regards,
Pedro
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