Sorry for the slow response, Jason, the last-minute huge duty changes by the government have taken up a lot our time and were completely unexpected!
I’m afraid that I cannot think of a good way (but I’m open to suggestions) of grouping tracked containers, as we would have to just guess which container was emptied/filled on a quantity change. If we guessed the wrong container (which is highly likely), then this would cause you problems down the line when it comes to racking and assigning them to deliveries.
Using non-returnable containers would, however, not have this limitation (although then you don’t get the same level of tracking of their locations/uplifts), and the stock take tool already supports grouping these.
It sounds like using pallets would solve this for you 
which is great news as this is already a project that we plan to do soon and would come with lots of other benefits (including assigning entire pallets to a delivery to reduce scanning at that stage). Please could you vote for the pallets feature request and we’ll use that as the solution for both the stock take too:
If you can get others in your team to vote for the pallets feature too, this will help make sure it’s high on the list 