Unless the gas in each cylinder was nominally the same mix, it wouldn't make sense to assume that whatever the end product of that would be something you would want to breath or to dive.
For example, if you had 21%(air) in one cylinder and 32% in the other cylinder and your analysis came up to 26.5%, based on what mix would you determine your no deco limits? Would you trust that the gas you are breathing is always 26.5% or would you plan on depth limits based on 32%?
In my mind, if you are in this situation, it is basically a fuster cluck and the best thing to do is not be a nickel rocket, dump one of the cylinders and then get proper fills.
If the gas in one or both of the cylinders is trimix, then it means you are thinking about doing a more "substantial" dive. And if your cylinders don't have nominally the same mix in this scenario, you have a giant fuster cluck even before you get in the water. The best thing would still be, fix it before you go diving. (Dump the contents of one of the cylinders into a stage bottle, etc.)