VersionSQL uses the VIEW SERVER STATE permission to identify whether the target server is part of a Sql Server Always On Availability Group or Cluster. If it is, VersionSQL uses the name of the availability group in the committed files’ folder structure instead of the name of the individual server to which it is connected.
This can be disabled from the VersionSQL->Settings menu, Advanced tab, by unchecking Replace server name with Availability Group name, if present.