1999 BMW 840 not starting after batteries flattened

The car had been started, driven out of garage - then back in some 6-7 weeks ago. Forgot to re-couple battery charger - but locked up vehicle. Accessed the batteries through opening the boot with 'skeleton' key, connected charger momentarily to left side battery and was then able to open the left door using the key remotely. Opened bonnet and connected the charger to the charging terminal. Re-charged batteries and attempted to start the engine. Engine span over strongly - but showed no signs of starting. Next I followed procedure for installing new batteries as per the manual by disconnecting the batteries neg. Terminals first then +ve's then reconnecting vice versa - but engine still won't start. Have I caused some damage by initially connecting charger to left battery only and, if so, what is it likely to be and how can I fix it? (I live a 180 mile land and ferry journey from nearest BMW dealer in Aberdeen).