Hi Melanie,
It sounds like this might be a different set of permissions that might be preventing you from seeing the other projects here. At least I'm inclined to believe this since it had been working and you mentioned cleaning up some project configurations recently.
I would recommend trying to use the Permissions helper in the admin section of Jira Cloud, you can also find this by going directly to https:// [yourCloudSite] .atlassian.net/secure/admin/PermissionHelperAdmin.jspa
Using this utility, I would want to make sure that the user account in question here has the create issue permission in the destination project. If they do, then try checking also for Assign issue, schedule issue, transition issue, for starters. Not all projects will require those specific permissions, but it's possible that one or more of your software projects might require these to be able to create issues in those projects, in addition to the link issues permission.
Certainly if the user doesn't have permissions to create issues in the destination project, that drop-down menu will not show you that project as an option.
Another way to test this would be to see if that user can create a new issues in the destination project using the + sign in the left navigation bar of Cloud. If they can't see that project there, then it's most likely a permission problem.
Please let me know the results.
Andy
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