The add-in manifest is accessed via its URL on installation and after that the XML for the manifest is stored in Exchange. In order to update the manifest in Exchange, you will need to install the add-in again using the same URL.
Exchange On-Premise
You can install add-ins for all users in an organization in Exchange through Exchange Control Panel for On-Premise users (Source).
Exchange Online / Office 365
You can install add-ins for users through centralized deployment for Office 365 users (Source). There are some considerations for deploying an add-in for Office 365:
- Users must be using Office 2016
- Users must be in the top level group, as nested groups are not supported.
- Users' mailboxes must be hosted in Exchange Multi-Tenant or Exchange Dedicated vNext
Outlook.com
In order to update add-in manifests for Outlook.com users, the manifest must be resubmitted to to the Office store.