Hi Devon,
In my experience, working with FXL is an absolute pain. Importing the new or updated FXL library removes all the attributes from the objects in the project, so it is never an option for us.
We have been nagging SITECH in Australia for a solution, and they responded by giving us extra functionality. "Vanilla" TBC FXL workflows are still terrible, but at least we have "workarounds" now.
If you want to add new attributes to any element, consider using the "Attribute Editor" from TBC's "ANZToolbox" Module. It will allow you to add new attributes, even if the initial pick-up was done using FXL without those attributes. Attribute Editor
If you just want to relayer objects (or change the layer names) in bulk, consider using "Map Objects" from TBC's "ANZToolbox" Module. Basically, it will allow you to change layer A to layer B in bulk, or move all Features "X" to layer "Y". Map Objects
I think you can request a 30-day trial code from SITECH to give that a go.
Best of luck.