Draw the circuit, the positive of the first parallel pack would connect to the positive of the second parallel pack, which because all 6 are also connected in series the positive of the first battery in the second pack is connected to the negative of the last battery in the first completing a closed circuit and shorting out the first 3 batteries. Same holds true of the joint negative of the two parallel packs which would short out the second pack.

I apologize, I misspoke when I suggested you wire 2 fans in parallel, they would both see 48 V with 1/2 amperage. You could wire 2 fans in series or yes they do make 48 to 24 volt step down transformers. You can Google same. Still think two fans each with its own isolated 3 battery circuit works best.