If your Shopify collection isn't being automatically re-indexed by Nacelle, this is likely because it is a "smart collection."
Smart collections are collections in Shopify that have conditions (equal to, less than, greater than, etc.) set. These collections unfortunately do not trigger webhooks, which Nacelle uses to listen for updates from Shopify. In these cases you'll have to manually re-index the collection.
Spotting a Smart Collection
This can be done two ways. First you can navigate to a specific collection in Shopify, and look for the Conditions section. Normally, this is located right above the Products list. Collections that aren't "Smart" will not have this section.
Alternatively, in your Shopify dashboard you can navigate to the Collections page, and filter by "Type." Select "Automated" to see a list of all Smart Collections.