Hi @RobStauder,
You can check you datastore cert by opening the url https://localhost:2443/arcgis/datastore then looking at the cert info.
You have two problems your ArcGIS Server is not functioning correctly and your Datastore is not validating.
First make a backup of the system
Then can you go to services and look which service account is running your ArcGIS server then reapply the security rights on the folder structure at c:\program files\arcgis\server and the location of you configstore c:\arcgisserver or d:\arcgisserver...
Service account
config-store
Program Files
right click and open server properties then security and your service account make sure it has full control on these folders, there is a new Windows policy that changes the service account to read only.
after you have applied this you can check if your ArcGIS server is functioning.
Then there might be a partial file that has been created during your failed publishing go to C:\arcgis\arcgisserver\config-store\services\Hosted and see if you can see anything also your rest and services will not work if this is the case
https://dns:6443/arcgis/rest
Datastore
if you can make a backup then @Ikebana suggestion will work and do a nice clean rebuild of datastore but your ArcGIS server must be in a working state.
You can also try the following go to server manager and unregister the datastore then re-register it on https://dns:2443/arcgis/datastore
you only have to unregister relational NB did you make the backups
using the https://dns:6443 admin url
if it still fails then go to the tool
"C:\Program Files\ArcGIS\DataStore\tools\unregisterdatastore.bat"
and try the 2443 url again
If it still fails then the only option left is to restore the backup
to create the backups run
"C:\Program Files\ArcGIS\DataStore\tools\backupdatastore.bat" --store relational
and
"C:\Program Files\ArcGIS\DataStore\tools\backupdatastore.bat" --store tileCache
please make sure that they did actual make a backup in the backup location
and
something like this for relational
to restore uninstall ArcGIS datastore and remove all the files except backup in c:\arcgisdatastore or your location
relational then edit and run these commands
"C:\Program Files\ArcGIS\DataStore\tools\restoredatastore.bat" --store relational --target most-recent --source-loc D:\arcgisdatastore\backup\relational --data-dir D:\arcgisdatastore --server-url https://dns:6443/arcgis --server-admin adminuser --server-password adminpassword --loaddata true --prompt no
tileCache
"C:\Program Files\ArcGIS\DataStore\tools\restoredatastore.bat" --store tileCache --target most-recent --source-loc D:\arcgisdatastore\backup\tilecache --data-dir D:\arcgisdatastore --server-url https://dns:6443/arcgis --server-admin adminuser --server-password adminpassword --loaddata true --prompt no
don't copy and past the above string type it out please you might get encoding problems
Regards
Henry