If you still have the working directory, you can re-run with
--reports-only to aggregate the reports. It is also safe to simply repeat the fmriprep command; if all steps finished correctly, it will simply check that the output directory hasn’t changed, and then construct the reports. (This might take a minute or two, depending on the size of your dataset, but it will also make sure that there aren’t unfinished steps that you failed to notice.)
If you do not still have the working directory, you’ll unfortunately need to rerun. Most, if not all, of the sub-reports require files from the working directory to reconstruct, and the sub-reports are stored in the working directory until they are aggregated into the output directory.