Yes, only Jira sites that have the Synchronize Attachments toggle enabled on the Connections page will have the attachment synced from the associated issues and Salesforce objects.
If there are two sites connected in the Salesforce environment, Jira Site A has turned on the Synchronize Attachments and Jira Site B turned it off, then Salesforce will only push/pull attachments from Jira Site A and not Jira Site B.
For more information on how to configure the attachment syncs, read Working with attachments in Salesforce.
- Is there any difference in setting up the integration in Jira for the multi-site feature?
- How do I connect more than one Jira connection in my Salesforce environment?
- How to view, create and associate Jira Issues from Salesforce by switching the Jira connection?
- Why can't I switch or view the Jira connection dropdown for the Lightning Aura and Visualforce components?
- What are the limitations of the multiple Jira site integration?