Hi Mike,
I played around with this a bit on my end. With SmartSDR for Mac (not sure about Windows), I can't manually enter values for the high/low cutoffs, but I can use the arrows to adjust. Using the arrows, the filter does remain in LSB. However, once the filter center goes above 0, the filter does change to be USB instead of LSB. Additionally I don't see any indication that the AppImage is trying to override any adjustments to the filters (other than when initially entering FDVU or FDVL).
Anyway, I suspect this is a Flex bug. (I'm testing with 4.0.1 FWIW.)
Thanks,
-Mooneer K6AQ