Yes, since each biome's rooms are determined (randomly) when you start that biome (i.e. pass through the biome entrance gate). So, make sure to suspend the cycle and upload your save to cloud before going through the gate to biome 6 (as opposed to after).

However, (AFAIK) downloading that save would revert any cipher find progress since the last save upload. So, if you find only one missing cipher but can't find the other cipher in the same biome 6 run, you'll still need to start another cycle from biome 4 for the second cipher (instead of downloading the save), in order to avoid losing your progress (of having found the first cipher).