Yes, one shipment can have cargo assigned to more than one FBA (Fulfillment by Amazon) location. Amazon will assign a different FBA ID for each fulfillment center, so your shipment may have multiple FBA IDs.
If your shipment is split into multiple fulfillment centers:
If you would prefer to send your Amazon shipment to a single fulfillment center, you can sign up for Amazon's inventory placement program.
See How to Ship to Amazon with Flexport for more information about shipping to Amazon.