Yes, I can see the problem. However, what you described is almost exactly what we do. Each brew is split equally into 2-3 fermentation vessels and we blend them back together in our racking tank (which is the only vessel we have big enough for a full brew), which averages out all the readings.
It seems that what we need is some sort of sub-gyle we can create to keep track of the separate readings. For example, we could create a new batch - say gyle 123 - transfer it into copper, so we get a recorded start volume, and then when we transfer it into three separate FVs we get gyles 123a, 123b, and 123c. Or perhaps we could have one FV set as the master gyle and then 123-2 and 123-3 for any subsequent gyles we transfer out after that?
The sub-gyles could also be kept, should we need to rack from just one of the vessels.
As far as the averaging goes, I would say that averaging out the readings proportionally by volume should work out fine. At the moment we simply say that 500 litres of 1.010 + 1000 litres of a 1.013 = a blended gravity of 1.012. The original gravity for the beers is the same, so working out the ABV should be straightforward too. Other readings should be just as straightforward, I think.
Another approach would be that should you blend beers back together, you could put a stop on any packaging until a new fermentation reading is done and entered onto Breww for the re-blended beer. Again, we would always take a blended reading before racking to ensure we have the correct final gravity recorded, so it would make sense from our perspective.
For the graphs and comparing batches, a sort of flow chart approach to readings with branching lines of the same colour that re-join when blended would be great, but I would be happy with an average reading across the whole fermentation, once the gyle is complete, if it is simpler to do.
Some sort of solution like this would make it much simpler to keep track of things for us, as at the moment, we are using workarounds to use Breww. Fermentation readings are obviously a large part of it, as I have to record everything on paper, work out an average to enter as our fermentation reading. I then enter the actual results in the notes. This gets more tricky on the day the vessels are put on chill though, as we end up with some vessels on chill before others, and knowing whether to still take an average or just enter the details for the FV that is still fermenting can be problematic.
Similarly, because we can only use one FV on Breww, I have to do similar things with the cleaning records too, making notes on which FVs were actually used when they were cleaned, and which pH reading is for which FV. All of this is especially fiddly, as I do most of the day to day recording on my phone.
Of course, if you have any ideas, I’d be happy to hear them, or any workarounds for problems, for now, would also be appreciated. For example, I’m already wondering why I don’t just transfer 1 litre from each brew into each of the other FVs we use, to trigger cleaning records! I’m sure there’s plenty of other things we could do too.