Yes - inverting the output in the Flex will do the same as swapping the speaker connections. Also your SVS sub will almost certainly have a phase switch or knob because it's a normal thing to check when setting up a sub, probably described in the SVS manual. If you've got the frequency and slope of the sub crossover correct then incorrect phase will show as a big dip at the crossover frequency, while correct phase would have a flat response, or at least flatter. You might be unlucky and have a room response null at crossover frequency, in which case it may be hard to spot the difference.
Oh, so I get a big dip when inverting phase, but not at the frequency I chose for crossover. I am new to using a sub and miniDsp etc so followed miniDsp instructions on setting up my Flex. I was a bit confused as to where they got their crossover frequency from in the online guide. I choose 85hz and to be honest it does drop on inversion but only by a few dB. But, at 103hz there’s a massive sharp drop on inversion. So, does that mean I should use 103hz as crossover and that the SVS sub is actually in phase with the V3 monos? All interesting stuff even if I don’t fully understand