I didn't feel it was nescasary to go into specifics and exactly how the mines would work, but seems it was needed.
I assume that instead of a general "don't blow up" signal the mines would probably need a password of sorts. Again, its not really that hard. So allied ships would have to broadcast something like this, "Bravo9445-T64Zeta, Temprorary disarm, Standby. This message would need to be on the right frequency and directed at a specific spot on the mine, and it would need to be done to every single mine in the area.
Notice the 3 parts of my little message. The first part is a password, that would only be known to people of certian levels of security clearence. The second part is the comand sent to the mine, you could also ask the mines for a status report, to self destruct, to phase in or out, or to rearm themselves. And last we have Standby, which means that the mines should be waiting for another command, in this case an order to rearm after the allied ships have passed through.
The password itself could change to another preset password every hour so some one would have to know the entire list to trick them into disarming. Different minefields would have different passwords, infact even different mines could have different passwords. Also you would need to know the location of every mine to be able to disarm them all, information you wouldn't have unless some one gave it to you. And finaly like most websites if you imput a wrong password 3 times in a row it could lock down for a certina amount of time.