It should not be a problem at all. During charging the two banks will have the voltage increase exactly the same and within limits of the charger. You will see more current going into the larger capacity bank, this is not a problem.
During discharge you will also see the voltage exactly the same and have more current from the larger capacity bank, again this is not a problem.
During rest when not charging and not discharging you could have current from one bank to the other (depending on what your charger is doing, assuming off), over time this could drain one of the banks a bit. This is also something that occurs when you mix new and old batteries, or mix LifePo4 with SLA (Sealed Lead Acid) types. This is only a problem if that current is high enough and over a long enough time that you could loose some of the charge.
I do this and I monitor the power in and out of each bank.
Randy