I've had some layers uploaded onto portal for a few months now, edits were made onto the layer without it affecting the data at the source. Today, I went to the layer and for some reason none of the data will load.
First I would start by identifying whether those layers are hosted or the datasets were copied to the server during the publishing process. That will add some direction to where to look next. If hosted content is having an issue, try validating the relational data store from Server Manager and see if it's healthy; if the data was copied to the file system, making sure permissions are in-tact for the ArcGIS Server service account would be a useful approach.
You also may be able to look at the service workspace for the affected services (if non-hosted) to determine where the data lives. Try clicking the database icon next to one of the affected services in Server Manager.