If you have two audio files loaded in separate panes, and they are aligned, then you should be able to take annotations made against one of them and copy/paste them onto the other one and SV will adjust their timings to match the alignment. This sounds like what you are asking for?
For example:
1. Load an audio file into a new session
2. Use "Import More Audio" to load another (presumably of the same work)
3. Switch on the Align control
4. Make sure the first pane is active, and tap some instants into it (e.g. with the ";" key)
5. Select all (e.g. Ctrl+A or Cmd+A) and copy to clipboard (Ctrl+C or Cmd+C)
6. Make the second pane active (by clicking on it)
7. Paste (Ctrl+V or Cmd+V)
SV should pop up a dialog saying "The instants you are pasting came from a layer with different source material from this one. Do you want to re-align them in time, to match the source material for this layer?" Say yes to this, and the instants should be pasted into the second pane with appropriate alignment.