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You can upgrade linkerd as instructed in the docs, making sure the identity.externalCA setting is enabled, and assuming the linkerd-identity-trust-roots ConfigMap is provisioned externally.
Note that if you're doing this through the CLI, the flag is --set identity.externalCA=true.
The dataplane pods will need to be restarted in order to pick the new trust root. The transition can cause downtime, but you can avoid that by bundling together the old and new cert, similarly as described here.

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Answer selected by miguelvr
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