Characters go missing

I had a fairly large number of Characters go missing. Under v2, they were Minor characters that were given no supporting Events or Dates. I set Ignore for them. But now they all were removed and on Syn they were transfered to the Trash in Scrivener. Why can’t I just ignore them as before?

Sorry that you have had your character files end up in Trash. Files get moved when syncing to Trash when the equivalent item in Aeon Timeline is deleted/removed.
To understand what has happened, are you able to clarify:
Before you synced, did your Aeon Timeline file and your Scrivener file both contain these minor characters? But then when you synced, they were deleted from Scrivener? Or did only Scrivener have them?
You can set documents in Scrivener to be ignored the first time they are synced. If you click on the document in the sync binder, in the inspector on the right under Linked Items->Timeline it will show what this document is going to be linked with (either it will create a new item, or link to an existing one). You can choose ignore from this list, and then this character will be ignored when syncing.