Keep in mind that any batteries simply connected in parallel (charger off) will naturally self equalize.
Let's say one battery reads 4.1V and the other is 3.9V, if you checked them a minute later both would now be at 4V. That said it's not recommended to parallel batteries with a wide difference in voltage, let's a 3.2V and 4.1V as there will be a large and quick flow of current from the high to the low one as they equalize possibly causing an issue.
I parallel charge 4 Li-ions at a time for various devices. I wait a minute before turning on the charger to let them equalize.