The spec's for an EM 5.7 states that they have a Lipo battery. I'm no expert, but making a parallel connection with two Lipo's of a very different state of charge is generally considered to not be a good idea, because of the rush of current from the higher to lower voltage battery.
With some experience using Lipo batteries on RC vehicles and E-bikes, 11.7v is considered dangerously low for a 12 cell Lipo(I'm guessing that might be what the EM 5.7 has). The recommended range for a Lipo cell is 2.8-4.2v, so assuming your 48v battery is made up of 12 cells, 33.6v would be the lowest.
Do you know if the battery has a BMS(battery monitoring system circuit board), 'cause a BMS is s'posed to prevent a battery made up of multiple cells from draining below recommended voltage levels?
Does the bike have a voltage meter telling you that the battery is 11.7v, or did you measure it with a multi-meter? If, by chance, the battery is made up of a configuration like 4 lots of 3 cells(i.e. 4 x 12v in series = 48v), then hopefully you got the 11.7v from reading just one lot of 3 cells, in which case 11.7v would have each cell at 3.9v, which is close to a full charge of 4.2v.
The guys on
https://endless-sphere.com/forums/ might be better suited to help you.