@BishopBob (great name btw!)
This seems very strange, there should be no correlation between scene recalls and the actual connection of expanders – though there can of course be differences in patching.
A few things to check:
When you have lost connection/signal, does the SQ show that nothing is connected (either at the top right of the screen or in the I/O screen)?
Have you tried enabling patching filters to prevent scene recalls from changing any patching?
Do you have anything connected to the USB or network port that could be sending control messages to the SQ that might change patching inadvertently?
Thanks,
Keith.