Never yet removed the battery to recharge it always left on car totally flat or just topping up, cant say I have had a problem after ! 
you have been very lucky by leaving it connected you are at risk of damaging the ecu,alternator and electrics,the gases of the battery can build up and explode and the battery can boil leak acid and cause lots of damage
mmmm let me see .. my alternator can shove out about 100 amps at a push (although it usually only goes to 30-40amps )... my battery charger only 6 amps .... the alternator is often connected and running for 5-6 hours (up to 12 on a South of France run)...
The alternator runs at 14.4 volts, the battery charger at 14.4 volts as well, so why would a battery charger do so much damage ??
A well maintained battery (clean connections, clear vents, correct electrolyte level) will suffer no damage at all from deep recharging by battery charger.
In a very rare circumstances, a "shorted" battery left charging unattended for a long period MAY, just MAY, cause problems