There's two layers to this
First, you need to change all the permissions on the projects you don't want them to see, so that they can't see them. (A common default is to use "JIRA users" as both the "can log in" and the default "users" role membership. Meaning all issues can be seen by all users by default. That's something you'd need to unpick)
Second, in the projects they can now see, implement issue security to lock down the issues you don't want them to see.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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