Jen,
Sorry for the delay. The default configuration for study reloading does not include lists, ever since we changed the study/folder archive structure to move the lists into the folder archive configuration. However, this is supported if you make the following changes to your pipeline files for the study folder you are reloading into (see the attached study zip archive from the LabKey demo study as an exmaple):

1. add a line to the study.xml file for a reference to where to find the lists directory (i.e. <lists dir="lists"/>)
2. add the lists directory to your pipeline (you can get a copy of the lists directory for your given study folder by going to the Admin > Folder > Management page and exporting the full folder archive with the Lists checkbox selected)

Give that a try and let me know if you have any issues.
Thanks,
Cory