Last week I was looted the Reclaimed Shadowstrike after killing Onyxia in the 10man mode. I immediately conjured the Thunderstrike to see what it looked like/the stats on it, but I destroyed it, thinking it functioned more like Benediction and the old Shadowstrike. Now, when I go to use the original, i recieve the message "no charges available", and it seems I have no way of summoning the other polearm back.

This charge system is probably a good idea to prevent duping of thunderstrike for tanking ferals (loot the shadowstrike to one, have them all make thunderstrike and trade shadowstrike) but couldn't the use on Shadowstrike just soulbind the item so that this doesn't happen?

Any resolution to this matter would be appreciated.

The item makes the additional item so that it is not difficult to enchant. You would need to enter an in-game ticket to speak with a game master about getting an item restored. I cannot however, tell you whether or not they will restore the item in this situation.