I've not had this issue in the past, and I'm not aware of having changed any settings.

I can't get the export menu to stay on the right side of the canvas when I switch between projects. It used to stay there if I didn't close it before closing the previous document, but now it disappears and I have to reopen it every time. This wouldn't be a huge issue except I am regularly exporting one to two hundred images (separate documents, not individual components of one project) for a stop-motion style animation I'm making, so it adds another entire step to this long, tedious process.

I tried looking in edit>preferences, but I couldn't find anything in there to help.

As a less significant issue, the program has stopped remembering the folder that I regularly export to, so I have to navigate my computer to select the correct folder every time.

I don't know if these issues are related, but any advice on how to streamline the exporting process in any way would be hugely appreciated.

Thanks for your time.

Do you already have multiple svg files saved ? 

There is a windows batch convert script on inkscape.org for this.