Thank you so much for taking the time to run a participant and confirm for us that it was not a problem with the data itself!
We tested a few more things in lab and it seems like it might have actually been a problem with our external hard drive, it is large enough to hold all of our data (8T) but it is quite old and when we opened it on a different computer, we saw that the permissions for reading and writing were a bit odd (“custom permissions” but no ability to modify them). So we tested having fMRIprep read the data from the hard drive and then write the working directories to a separate drive. This seems to have solved the problem - we have successfully run 3 participants (without free surfer, under 1.5 hours per participant) with no errors thus far using this approach, so it seems like it might be the solution. We are running a batch of participants overnight and if any errors come up we will share them, but fingers crossed we are good to go!