I suppose there are good reasons to not mix them.
However, if the cans are all partially used and the batches are satisfactory and haven't spoiled due to poor storage, then I don't see what the harm is to consolidate them. My older full can of Goex doesn't have much air space, maybe 1 inch or less. It's just enough room to tip the can before it will start pouring out.
The only other concern would be to homogenize the contents of each can by mixing them up. One way to do that might be to transfer partial amounts back and forth into each partially empty can several times until you're satisfied that the powder is well mixed. Not that there's much of difference per can, but there might be more fines in the bottom of one can than the other. At least mix the fines up.
I wouldn't recommend losing track of the batch if you were shooting in competition and wanted to keep it separate for performance reasons.
But as long as the batches haven't had any quality issues or concerns, mix them, and you can always record all of the lot numbers etc...if you really want to.
When it comes to substitute powders I'm more of a purist. Some batches can be quite old and their potency or formula might have changed over the years. But since black powder doesn't usually have qualititative problems as often as the subs, I wouldn't worry about it.
You're not going to smoke a cigarette while transferring it are you?