Using version 0.6.6 of fmriprep, I tried to run a batch of ~60 subjects on a cluster.
These ran until recon-all, and then failed when the BIDS/derivatives/freesurfer/fsaverage directory couldn’t be found/created. 
I manually created that directory, then ran fmriprep again, and this time the subjects all completed recon-all, then a sampler node failed during mri_vol2surf because the fsaverage5 directory could not be found. 
I manually copied the fsaverage5 directory into the appropriate location, then reran fMRIprep, but nothing seems to happen. fmriprep launches, warns me about missing fieldmaps, builds a base workflow for each BOLD run, then completes. 
So, my footnoted questions:
1,2 – I assume that fmriprep is supposed to create the fsaverage and fsaverage5 directories, and this seems to have worked when I ran a single subject for a different dataset. Any idea why it’d fail for a batch of subjects?
3 – I’d thought that after a nipype crash, rerunning the workflow would pick up where it left off. This seems to not be happening. Any thoughts on how to resolve it? I can delete my working directory, which I think will force it to rerun a bunch of time-consuming steps, but I’d rather not re-run the recon-alls.