The only workaround I've found is to compose a single snapshot's worth of patterns, but write them with the assumption that you will switch samplebanks at some point. Switching samplebanks can be done without stopping the sequencer.
So put all your patterns that use the samples in the first samplebank into (for example) A01-D16, then ones that use a second bank into E01-H16. Before performing the patterns in E-H, you'll have to menu dive in order to switch the samplebanks manually, but it's not difficult.
My one recommendation is: When you make the switchover, have a pattern running that uses only internal machines, unless you like the brief cacophony that will ensue otherwise