Command status is handled by addon.ini. Open it with notepad or similar and change the commands to whatever status level you want them to be.
To fix item charges try this:
UPDATE items SET SpellCharges=1 WHERE SpellCharges=0;
And by "summon" I hope you mean #summonitem, because all items summoned using spells are no rent and should disappear when you log.
I know there was a bug quite a few versions ago that would cause you to lose items while zoning although it hasn't happened to me in quite some time and this version seems to work fine. Perhaps there is an error in your items table somewhere?
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