While I have a tendency to believe that your battery is weakened. It is very hard to tell without knowing your charger specifics (Brand/model number or its charge specifications), and/or performing a load test on the battery. Knowing the specific gravity of the electrolyte would help, too.
Does your bike have the stock electrical loads? Halogen HI watt headlight? Dyna coils?
To restore a good battery to full charge state takes about 120% of the energy removed. The chemical to electrical conversion is not 100% efficient in either direction. So, you have to put in more than you take out. A deeply discharged battery will take much longer to peak up than a partially discharged battery. I have a yuasa smart charger that will take 2 days to charge up to the 14.5v peak when my 550 batteries are run down deeply. However, if I boost it first with a 6 Amp charger for 15-20 minutes, it only takes a few hour for the Yuasa Charger to finish the peak up job. WARNING! I can cheat this way because I know what voltages to look for and what signs the battery/meter gives during the charging process. If you do this fast charging wrong, you can damage the battery permanently.
The stock battery is rated at 12V - 14AH (amp hours) This roughly means it will supply a 14 amp load for 1 hour. The stock bike, at idle draws about 6.5 amps from the battery. So, in theory the bike with all its lights on can sit and idle for a bit over an hour before the battery drains enough that the voltage is too low to fire the spark plugs. Obviously, a weakened battery won't last that long. Further, the electric starter draws 150 amps while it is engaged, and that takes a bunch of the battery capacity away with it's use. The alternator has to run above 2k RPM about 10-20 times longer than the starter was used, just to put back the energy used by the electric starter. (again assuming the stock electrical components)
Without knowing how long or how deeply you operated your battery in depletion mode, or how much energy you have put back into the battery, it isn't easy to predict with certainty if your battery is damaged.
Cheers,