You may get an earlier answer but Captv8tr is most likely the person best suited to answer this. He's American and they get up later than much of the rest of the world.
Give it six hours or so and I'm sure he'll be able to help, if no one else can meantime.
See www.grainge.org for RoboHelp and Authoring information
How much influence do you have with the Captivate content?
I ask, because Captivate is similar to RoboHelp from the standpoint of editing content in Captivate, then producing different outputs from the content. Of course, SWF is one output type, but you also have HTML 5 output AND Responsive HTML 5 output as well.
From what you have described, you are simply adding the Captivate content to baggage, then doing things in RoboHelp to link to it. This leads me to believe that you are possibly bypassing the dialog in RoboHelp that allows you to insert Captivate.
When you use this dialog to insert the Captivate, you have the option of pointing at just the SWF file (if you use the bottom field with "Multimedia Name" to the left) or you point at the index.html file (if you use the top field with "HTML 5 Output" to the left).
Upon clicking the OK button, depending on what you selected earlier in those fields, either the SWF will be copied to the project and added to Baggage, or the swarm of output files will be compressed into a single CPZ file and added to Baggage.
In no case should the Baggage files be conflicting, assuming you are using this dialog.
If you are going the manually added to Baggage route, that's entirely possible. If you prefer this approach, my own suggestion would be to create a new, distinct, folder for each Captivate output you will be adding. Then add the files and folders to that new folder.
Hopefully something here was marginally helpful.
Thats great thanks - worked perfectly! I had abandoned that method of importing captivate content as it was placing a .swf placeholder and didn't appear to work if only importing a html5 file! Having tested this thoroughly using only the HTML5 file from captivate I'm able to place multiple projects in robohelp WITHOUT flash content - albeit still a little slow to load.