Permanent loss requires you to lose the private key associated. Please tell me how is it possible to lose the key when you have 2 copies of the wallet containing it?
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The biggest problem arises after 100 addresses have been used.  Since Bitcoin-Qt generates random private keys instead of using a deterministic algorithm, the change from the transaction will be sent to an address that only exists in one copy of the wallet.  As such you no longer have "2 copies" of the private key.  You only have one.  Now if you are sending transactions from both wallets, you'll end up with some bitcoins only associated with addresses in one copy, some bitcoins only associated with addresses in the other copy, and some bitcoins associated with addresses in both copies.  The average non-technical user who has been happily using their two copies of the wallet without seeing any issues suddenly notices that the two copies of the wallet no longer have the same amount of bitcoins, but has no understanding of how or why this has happened.  What they do next to attempt to resolve this issue on their own carries risk of losing the private keys from one of the copies of the wallet (and as such all the bitcoins associated with private keys that only belonged to that "copy").

In addition, since Bitcoin-Qt will let you send transactions when the blockchain is not fully synchronized, it becomes easy to accidentally double-spend the same transaction output.  This results in a reduction in apparent balance, and a transaction that will never confirm.  The user can use the pywallet program to remove the bad transaction from one copy of the wallet if they are aware of that tool, but the point is that the wallet isn't designed to be used in this way you are very likely to end up with a lot of inconvenience.