There is no gameplay way to get the flasks after Elrath is arrested. However, you can get back in the basement either by hex editing (
Teleporting Anywhere) or file swapping (
FIX for the Missing Catacombs Portal).
Alternately, you can just get another set of potions (
Lost Items - guide and directory of inventory files).
By design there are only 2 cure potions in the game, but 3 victims. You can Pickpocket (level 2) a potion back from a cured person, kill one after curing (with no loss of reputation) to get them to drop the potion, or duplicate the potions before using either.
To copy a stackable item
Drag a stack out of (or into) your inventory (or container) and hold down the control key before dropping. This will bring up the split stack pane; type in a negative number and hit enter (the checkmark will be greyed out). This can also be done in the trade window.
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