Did you mean you set the depth for the piece from 0.0625 to 0.125? You wrote it the other way around I think, and the estimated time should not increase if you lower the depth required to be removed.
It makes sense to me that the carve time would more than double if you double the depth that needs to be cut and leave DOC for the bit where it was. Basically, you will get the tool path time times two plus added Z travel.
I do agree that Easel’s estimated time can be way, way off at times though. It seems most likely, at least based on my experience, that the estimated time is based almost exclusively on the number of operations remaining instead of each operation multiplied by an approximated time using the settings being used. For instance, when I milled out my new Z-Axis plates the estimated time remained almost unchanged the entire time a large rectangular piece was being milled out. There were not a lot of operations to be performed; there were just rectangles that needed to be carved. As soon as that section was completed, the estimated time jumped by about two hours.
Obviously, I am not aware of how Inventables is calculating the carve time, but there are certain instances where it is out to lunch.