What Paulo Coelho means is that through erosion ("the force of flowing water"), whatever is buried may be brought to light (like finding gemstones such as the emerald underground). Time eventually reveals all things, no matter how "buried" they may be. On a symbolic level, that includes all actions committed, all words spoken, all words written... nearly everything comes to light with the passage of time. These are the "treasures uncovered".
However, just like the water eroding away to uncover what is buried, that same erosion can cause landslides or mudslides that could bury something. Caves and mines collapse and treasures are lost. Sometimes, something that is precious to us is lost through careless acts (like leaving something lying around that could end up getting lost), or else it is taken away by outside forces. In this case, we know what has been lost, but we struggle with how to get it back before it is lost forever. These are the treasures that are "buried by the same currents". It also falls into the adage of "The Lord giveth and the Lord taketh away".
In my copy of The Alchemist the story of the miner and the emerald is on page 24.
Could you happen to tell me where in the book you found this passage?