The second replicated version always overwrites the first one on Azure append/page blob.
A workaround to the problem is to introduce an insignificant change to the file after it has been
initially replicated on the Azure append/page blob (such as an added interval at the end of a text
document, for example) in order to trigger versioning for that file from that change onwards. From the second version onwards versioning works as expected on Azure append and page blobs.
The problem is not present when your replication target is Azure block blob.