It's fine. I have done it. Usually, on a bass that can be strung both ways, I put at least the G string through the bridge to get a little more down force on the bridge saddle, to help boost sustain and tame twang, and at least the B and E top loaded so they don't bind or kink the core. I have strung the A and D both ways, depending on the string and what sounds good in relation to the others.