Forms clearing unintentionally

We have Government created pdf forms that we recently migrated from a file share to SharePoint online.  Our users are able to open the forms through Reader (Add a storage account > SharePoint Site), however when opening a form that has already been completed, the form will clear all fields.  We have been restoring the version history to the original through SharePoint which is obviously causing some frustration due to lost data.  Has anyone else experienced this before?