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I can confirm that the code in the PowerShell example only exports the first certificate with a private key, as originally reported. I'd request that this be re-opened.
I exported the certificate according to the code, as well as through the Portal (pfx).
For both, I extracted the certificates as PEM using this command:
openssl pkcs12 -in cert.pfx -out keyStore.pem -nodes -nokeys
Then when viewing in a text editor, the file produced using PowerShell contains only 1 entry, however the file downloaded in the Portal contains 2.
I believe the object type needs to be created as a X509Certificate2Collection to allow for the full certificate chain.
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