From looking at the screenshots you sent, I think the problem is that when you add or remove a Client in Collection #1, the same change appears in Collection #2.

And I've reproduced that problem.  It occurs if you make a copy of the .bmco document package using a file manager such as the Finder.  To verify this, open Collection #1 and click in the main menu: Bookmarks > Document Information.  In the sheet which opens, note the Unique Identifier near the bottom.  Do the same with Collection #2.  If the Unique Identifier is the same as in Collection #1, that is the problem.  Our apps use the Unique Identifier to associate a Collection with its Local Settings.  Same identifier means same Local Settings.

The simplest fix would be for you to activate the window of the Collection which you've put the least time and effort into, and then click in the main menu: File > Close and Trash.  Then create a new Collection by clicking in the menu: File > New Collection.

There is an alternative fix which would retain all data (except the Local Settings of course), but it is quite complicated.  I shall not explain that alternative unless you really want it because you have put substantial time and effort into both Collections, which I think is unlikely.

If you want to copy the Content (bookmarks and folders) from one Collection to a New Collection, create the New Collection as Empty, then use copy/paste, drag-and-drop, or perform a secondary click on selected items and from the contextual menu use Copy to….

Hello, Craiglea.  Thank you for contacting us.

Any setting in the Settings tab of a .bmco Collection document window should affect only that Collection.  This includes the Local settings.  In fact, the Local Settings are even more restricted: Local Settings will not propagate if you open that Collection in another Macintosh user account and/or on another Mac.

Maybe I'm not understanding the whole picture there.

What are the Clients in your Collection #1?
What are the Clients in Collection #2?

Give me an example or two of a setting which you see being reflected between collections.