BookMacster only affects web browsers like Safari when you click in its main menu: File > Export to…, or if you have enabled Syncing.  Syncing will export to all configured browsers whenever bookmarks changes make it necessary, after you have closed the document and/or quit BookMacster.  Syncing works in the background.

To verify that none of our apps are syncing with web browsers,

• Run BookMacster, Synkmark or Smarky.
• In the main menu, click the application menu (BookMacster, Synkmark or Smarky).
• Verify that, in the menu which appears, the Stop all syncing now menu item is disabled and indicates Nothing to stop.

You can also see the status of Syncing by looking at the Syncing button in the document toolbar, but this does not reflect syncing by other bmco documents which you may have created.  The Stop all syncing now menu item indicates syncing status for all documents, even if they are closed, and even further, all of our syncing-capable apps (BookMacster, Synkmark, Smarky).

Repeated reappearance of deleted bookmark items in Safari indicates that your iCloud is on the fritz.  We have a support article which explains that, and how to fix it.