Hello @zen-dsgnr, I'd like to try to help. It sounds like you're saying your institution uses a separate Canvas instance connected to Catalog than the normal Canvas instance your institution uses. Is this correct? My institute does this as well. We have a for-credit instance of Canvas and a non-credit instance of Canvas that is connected to Catalog.
You've used the term Media Galleries and I'm having a difficult time fully understanding what you're referring to. Our Canvas courses don't have "Media Galleries" they have a Files section. Is that what you're referring to? Or are you using an LTI tool for the Media Galleries? If you're referring to the Files section, my experience is that everything in Files gets exported from a Canvas course when doing an Export.
Speaking of Export, are you exporting the course through the Course settings (which creates an imscc file you can download)? When I do that, I can download the imscc file and then import it into a new course (in any Canvas instance). Is this what you're trying to do?
Regards,
Adam