Hi Reva90,
Thank you for using the Apple Support Communities. I see you have a question about your files in iCloud Drive.
Have you noticed any pattern as to which of your folders shows the modified date of 1969? For example, content synced from a third-party service like Google Drive or Dropbox, files/folders that were added to iCloud Drive from a specific device, or any other common factors?
Do you see the date of 1969 on all of your synced devices?
On the iPhone in question, tap Settings > General > Date & Time; is "Set Automatically" turned on here?
You mentioned this happened after updating to the latest version of iOS; to confirm, is that iOS 12.3.1 under Settings > General > About?
Regarding the missing documents, do you see them if you Use iCloud.com and sign in with your Apple ID there?
I hope this helps get you started. Kind regards.