Recently, Synplant has started saving all of my user patches as .fxb files instead of the usual .synp ones. Normally this wouldn't bother me, but it seems I can only use one file type per project, meaning I have to choose between my .fxb presets and .synp ones. Obviously this is a huge pain, so is there any way to get all of my presets to save under the same file type (ideally .synp)?

You get .fxb files when you save from the host. To save .synp files you need to save inside Synplant using the main menu.