If you use a courage stone to change the weapons physical attack one of the following will occur.
-You Physical damage % will change
-Your physical damage % will change, as will another random other stat on your weapon(chance of this one depends on the % of assimilation the stone has, the lower the better)
-The stone will fail.
You won't lose your +3.
BTW to the poster above, courage stones change white stats, not blue stats, so it won't become blue. Yes it could change a blue attribute if the weapon has one already but it won't add any if it doesn't have any already.
Good luck. And be prepared to be using a lot more than 1 stone

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Ooh, I got a sexy ex-staff title!