found a slight fix to this for anyone that might be interested; currently using 5.2. This works best on the assumption you’re exporting from 3D modelling software yourself, using consistent material slot names, like modular kits for example.
I imported all FBX with ‘create materials’ on then put the put these new materials into the same content folder as the materials i wanted to replace them with (so all in a collective ‘mat’ folder). I selected the two matching materials, so, ‘bricks_1’ for example that was imported with my FBX, and ‘MI_bricks_1’ thats an instanced version of my MM, then went to asset actions → replace references. In the pop up, you select whichever one you WANT to be assigned to your material. So I select my ‘MI_bricks_1’, which then replaces the ‘bricks_1’ reference across everything that uses that material.
Obviously, it only works across the board if your materials are named in uniform with each other upon export into UE. Hope that helps someone!