I have no idea how to solve the problem itself, someone else might help you there. But here's a way to bypass the problem by telling Debian to overwrite the file on each startup. It might work. Copy the file you want to preserve to somewhere else. In this example I've copied etc/network/interface to /opt/interface. Now, in /etc/rc.local add this line: cp /opt/interface /etc/network/interface I hope this helps.
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