...Also how long did you crank it with the new battery before you checked for the spark?
With electronic ignition on the 650 there is a voltage threshold the battery must stay above for the ignition to fire. If you have a weak battery, or you crank a good battery down, then while cranking the starter if the voltage falls below the threshold the ignition will not fire - you will have no spark.
If your bike was running normally when your battery went soft you can usually push start the bike to get it going, because the starter puts a huge load on the battery, and will pull a weak battery down while cranking, but if you push start it the ignition does not draw very much current.
A good indication is to look at the neutral light on the bike and your headlight - if they both go very dim or go out while you are cranking the starter, your battery is not holding up. It could also be due to a bad connection on the battery, or the ground wire from the battery to the frame of the bike being corroded.
To answer your question, a battery going dead on the bike will not do any harm to anything on the bike, it went dead on its own from sitting for so long without being recharged from time to time.
Its also very unlikely for the ignition on a 650 to fail - they are very simple and very reliable. So before you start pulling the ignition parts off the bike make sure you really do not have any spark.
Last edited by KCW; 12-19-2017 at 08:07 AM.