I was able to contact Cato off-list and we easily got back Cato's Safari bookmarks and his Firefox bookmarks using BookMacster's built-in Sync Snapshots, as explained in this support article.

After reviewing Cato's logs, it appears this is what happened:

• Cato created a document with Clients Safari and Firefox.
• When asked to import bookmarks, Cato clicked Later

So at this point, Cato had an empty document.

• Cato then commanded BookMacster to export this empty document to Safari and Firefox.
• A warning appeared explaining that the contents of this empty document would replace Cato's Safari and Firefox bookmarks.
• Cato clicked Export again.
• Cato was surprised when Safari and Firefox were then empty.

To prevent this from happening to other users, we did some work on that warning.  It has been reworded so that it is more dire and foreboding, and an additional warning now appears if the number of bookmarks to be exported is less than 5 when bookmarks are being overwritten.  The new and old warnings are shown in the attachment.

By the way, it is possible to not delete bookmarks during an export, in the Clients tab, under the Advanced Settings (gear/cog) button, by switching off the checkbox Delete Unmatched Items.  But this is not the default setting, because in normal syncing, users expect items deleted in the source to be deleted in the destination.