In Sitecore Experience Commerce 9, the way you rebuild Commerce indexes (used by Order/Customer/Catalog Manager in Commerce 8.2.1 and Business Tools in XC9) has changed. Here's a quick rundown of the difference:
Sitecore Commerce 8.2.1
Commerce indexes are defined in Sitecore and can be rebuilt via the Indexing Manager in the Sitecore Control Panel.
Sitecore Experience Commerce 9
Commerce indexes are moved outside of Sitecore and rebuilds are done by indexing minions in the Commerce engine and not in Sitecore indexing manager. Index rebuilds need to be triggered via API calls: