Eneloop batteries are NOT Li-on batteries and do not have a electronic circuit inside the battery that makes it impossible to charge it. It shuts it off, and no quick charger for AA batteries is going to help.
The solution: take 1 x old LP-E6 and connect 2 x pins (one into +ve and other into -ve) into the rectangular sockets. Take 2 short lengths of insulated electric cable and wrap around the pins or use dragon clips. Repeat at the other end of the cable, this time into the good/working (fully charged) LP-E6.
Charge should flow from strong battery to weak. After say, 30 secs, you might have enough voltage in old battery to allow the charger to commence re-charging again.
You cannot use nimh technology for li-on batteries.
I've done the above mentioned method for 3.7V Li- batteries with protection circuit inside, and it worked.
I can't guarantee it'll work with LP-E6s, the protection circuit could be different, but worth the try.
However, if they were too low voltage for too long period of time, the performance is significantly reduced. You can still use them if you're able to recover them, just keep in mind that they might give you even 50% or less capacity than they used to give.
-If possible, find a power supply with current limiter, and set it at nominal voltage (or just a tick over) and e.g. 500mA. Use that for 15 seconds at a time, and measure voltage in between. Limiting the current helps to prevent any accidents.
-If no such device available, use the cables as mentioned connecting to another (fresh) battery but only short durations at a time. LP-E6 should be able to give out several amps, and you don't want to keep that for long.
-It might be the protection circuit doesn't allow such raw charging method, so it might not do anything