60% charge (i.e 40% discharge) isn't really deep discharge. Deep discharge batteries are designed to work with 50% to 80% discharge cycles.
Typically a car (or bike) battery is happiest with no more than a 20% discharge but a occasional 40% discharge followed by quick recharging to 100% charge, while not exactly good for the battery, probably isn't going to hurt it much.
As I said, the best condition for a car or bike battery is 100% charge and recharging to that point immediately after use. When everything is working well, the amount of charge used to start the engine will be quickly recovered by the charging system. When you're actually riding, the generator is providing the power, not the battery. The battery is in the circuit of course and acts to smooth out voltage variations and any spikes from the generator, but the generator is doing all the work. The only time the battery might be discharging (other than starting) is when the engine is idling (or off) and you have a lot of power draw (headlights plus turn signals plus brake light + accessories).
You will get maximum life from a battery if it's kept at 100% charge and never allowed to go below 10-20% discharge. Mild deeper discharges will slightly shorten the life but not by very much If you leave the bike with the lights on and the engine off and the battery fully discharges, then you have hurt it. Charge it back up right away and you'll probably be fine, but the life of the battery will have been shortened. If you leave it in that discharged state for days or weeks, it could kill the battery completely.
1990 Kawasaki Ninja 250 (Rebuilt)
2011 Suzuki DL650A