Hi Fiona,
Thanks for your reply, and yes, I am having the same struggle as yours most possibly due to the interactions of strides between T1 and b0s. The pipeline I used generated topup_fieldcoeff.nii.gz with anterior-posterior being reversed (see below; look for the eyeballs in posterior!). I am not sure whether Left-Right was also distorted or not. This resulted in an extreme distortion in the preprocessing step.
So, what I did was to run fslreorient2std on both b0 and T1 in the INPUT folder, rerun Synb0 without any flags, and then pass the topup outputs to the dwifslpreproc.
The results are so far so good!
Amir