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If you created the stack using terraform (like me), that's an issue in the provider... Some of them have been fixed. Have a look: https://github.com/hashicorp/terraform-provider-aws/issues?q=bedrock+knowledge+base
Anyway, I had the same issue using the Action Groups and I noticed that if you create an Agent Version from the AWS Console UI it gets associated to the Action Group. While using CLI or terraform it does not. Probably the same happens for knowledge-bases.
You can cross check that: on the AWS Console UI, click on a Agent Version, scroll down the page an check if the knowledge-base is there.
Also, there is CLI command to associate the knowledge-base to an agent version:
associate-agent-knowledge-base \
--agent-id <value> \
--agent-version <value> \
--description <value> \
--knowledge-base-id <value>
answered a year ago
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