I have a 2000 Audi A6 Avant 2.5 diesel whose current Audi battery (approx. 650 CCA) is dying. Am looking at an Exide X-Tra Plus at 900 CCA to replace it. However, should I be concerned that the alternator can't handle the recharge in this and, instead, go with a lower CCA? The car has a warm start problem - hence wanting a higher crank-capacity battery.
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No, your alternator will not have any trouble keeping the higher CCA battery charged.
The alternator will quite happily charge the battery, but remember that it will take longer to do so, so if you run the battery down when trying to start it, it'll be longer before it is fully charged again.
There won't be any damage to the battery from using a lower-powered alternator to charge it, but there might be if you keep it at a low charge (e.g. doing lots of short journeys with loads of other electrical things on, so it doesn't get fully charged before you switch the car off)
What you have to be concerned about regarding the alternator is the amperage usage of your components VS amperage output of the alternator.
If you have a 100A alternator and your the standard draw of your components is 40A and max of say 80A (A/C on, headlights, wipers, rear defrost, stereo, etc), then your alternator will have sufficient additional power to charge the battery.
Even if turning on some of the heavier usage components puts your amperage draw over what your alternator puts out it will be ok for a period of time as it will draw that energy from the battery, but too long and you will be in a tough spot.
As long as you haven't added aftermarket components (new stereo, amp, speakers, HID headlamps, offroad lights, power inverter powering a 50" flat screen in the trunk (j/k, maybe...)) then your alternator output should cover the power draw of the car's components and the battery will be fine.
As mentioned, a higher capacity battery will take a longer period of time to charge up and this again depends heavily on how much excess amperage there is (Alternator Amps - Component Usage).