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Thank you for reaching out to the Jira Align Community.
Currently next generation and classic projects will behave differently when integrated with Jira Align. Classic projects in Jira Software have issuetypes and custom fields that span multiple projects while next generation projects in Jira Software have unique issuetypes and custom fields for each project.
Jira Align is currently setup to support a single ID for issuetypes and custom fields, but is reviewing the necessary updates to support the mass integration of next generation Jira Software projects.
There is a request to allow custom fields to span across next generation projects in Jira Software here: https://jira.atlassian.com/browse/JRACLOUD-71712