More cooling is good but I haven't heard of any EBR charging issues. I'd consider it an anomaly* and re-install to factory spec. In fact, I had a long conversation with an engineer at EBR regarding a draw I had (when mine was new in 2014) and he went long lengths to tell me they worked VERY hard to eliminate any draw or charging issues, considering the beating they took on the 2009 1125's.
*If you're keeping your battery topped off with a QUALITY charger, or using it regularly, you're all good. If you're abusing the charging system, who knows. Remember ANY motorcycle charging system (and most cars) are NOT meant to charge a battery from depletion. Excessive heat and burned VR diodes will happen when treated like that. For example, if it's sitting long enough to barely start (or need a jump to start) then you go right for a rip down the highwaythat stator and VR will get red hot trying to run the bike and fill an empty battery.