Here's some info from a guy who works with LA/SLA/AGM batteries on a fairly regular basis:
Most auto batteries will be what's called short cycle/starting cycle. Meaning they have a higher cold cranking amperage (CCA) and cranking amperage (CA), versus their amp hour capacitance such as an AGM or deep cycle battery.
A battery is basically a capacitor; it stores electrons. Now, the main difference between a capacitor and a battery is the fact that batteries are way more chemically sensitive to discharge. Both can be damaged by overcharging conditions.
With a short cycle battery, deep discharging can damage the plates mostly from the fact that the plates are thinner, and sandwiched together in a membrane. This allows the transfer of ions to damage the plates, which are easier to damage. This is also known as sulfation (or lead sulfate crystals). The more damage occurs the longer the battery is held at deep discharge. Typically a battery of this type, that has been thoroughly discharged, will give a much shortened life span. You might be able to "revive" it by using a battery desulfator that injects a rippled current into the battery (HF AC current or a rippled DC current) at timed intervals. I've had mixed results when busting open old batteries and seeing what they looked like.
Deep cycle batteries (AGM included) are much better at discharging cycles, simply because the plates are usually thicker, solid, and contain other rare earth metals to help with the sulfation issue. AGM simply is the same as a deep cycle, but can also provide even longer lasting results by using a fiberglass mat that contains the lead substrate. These are mostly used in areas where there is a lot of vibration. However, manufacturers do make starting grade AGM batteries. I've got one; the Deka Intimidator.
As a rule of thumb: Short cycle/starting cycle batteries --- only discharge to ~50%. Deep cycle/AGM --- only discharge to ~20%.
So to go back to your concern -- Yes, discharging the battery flat did reduce it's life expectancy. Should you be concerned? No. Just use it till it doesn't work no more, then change it. UNLESS it is meant for critical applications such as fire/ambulance/police or other life safety device.