I usually only download from one, but sometimes I download from both.
I don't care if the dive numbers in the individual computer logs are the same. I have no use for those numbers and never look at them anyway. I have multiple computers and use different ones for different things. It makes no sense (for me, anyway) to pay any attention to the dive numbers in the individual dive computers' logs.
What IS important is that all my dive computers are set to the same date/time. I try to keep mine within 1 minute or so of each other, but within probably 5 minutes is really fine.
I only use Subsurface for my log.
When I download from multiple computers, Subsurface automatically merges dives that start at the same time (within a couple of minutes or so - I don't remember the exact criteria). Thus, even if I used 3 computers and downloaded from them all, it still only shows as one dive in my dive log (in Subsurface).
When I view any given dive, it shows me the actual profile from one of the computers. If I want to see the profile from a different computer from the same dive, I can use the right/left arrow keys to scroll through which computer's dive profile is displayed. It says down in the corner of the displayed dive profile which computer it's from.
I'm not SURE which computer's profile it shows by default. I'm guessing it's whichever computer I downloaded from first. But, I really don't care. The differences in them are very small, so it does not generally matter to me which one is displayed.
A reason why I might particularly want to download from 2 computers for the same dive is when I'm diving my rEvo. I download from the controller, so my log shows me the pO2 Setpoint and the sensor readings from all the cells on the controller. I also download from my monitor (a NERD2), which brings in the AI data that shows me what my Dil and O2 cylinder pressures were during the dive.
Also, sometimes I dive with a Teric when I'm on CCR, as a standalone backup. Then, I only use my Terics when I'm diving OC. So, when I download my OC dives from my Teric, it also brings in any CCR dives that I did where I took the Teric along. When that happens, as I said, Subsurface automatically merges the Teric data from the CCR dives into the CCR dives that I already downloaded from my Predator (controller) and maybe also my NERD2.