I've got ~/Library/Safari/Bookmarks.plist, and I had ~/Library/STP/Bookmarks.plist, and as I said, even after I trashed the latter, replaced it with the former, and did a cold start, STP still reported the same bookmarks as were in the trashed file.
I have the ~/Library/Safari/Bookmarks.plist that contains all my bookmarks, but I do not have the corresponding file in ~/Library/SafariTechnologyPreview/ which is what I expected, but that doesn't explain why you have the Bookmarks.plist in both folders and I don't. To be truthul, I have used SafariTechnologyPreview off and on for years and I may have performed some step that I have long since forgotten. You might try copying the Bookmarks.plist from ~/Library/Safari to ~/Library/SafariTechnologyPreview and see if the full set of bookmarks shows up in STP.
When you trashed the Bookmarks.plist, did you also delete ~/Library/Saved Application State/com.apple.SafariTechnologyPreview.savedstate? That might account for the restored bookmarks.
