Schottky diodes for dissimilar Ah e-bike parallel batteries
You can connect two batteries like this ...







simulate this circuit &ndash; Schematic created using CircuitLab

... and the higher voltage one will power the load, until the voltages equalise and then they will both share the load current. 

Neither battery will be able to damage the other in any way.

The batteries should be the same nominal voltage, otherwise you won't gain the benefit of both their capacities. For instance if you have a 2S and a 3S lithium, your load voltage would have to drop to a damagingly low voltage for the 3S before the 2S made much contribution at all.

Of course, as Chris pointed out in comments, the batteries now can't accept regenerative braking from the controller. This still won't damage the batteries, but it might upset the operation of the e-bike.