Resolving an Error When Deleting a SharePoint Web Application Caused by Orphaned Databases

I recently encountered a frustrating SharePoint issue that I hadn't seen in many years and had almost forgotten about. It's a rare problem, but it resurfaced while I was configuring a new SharePoint Subscription Edition farm: I was unable to delete a web application, neither through Central Administration nor with PowerShell:

The root cause of this error isn't clear, and the usual troubleshooting steps are ineffective. I tried finding the associated timer job, restarting all SPTimerV4 and SPAdminV4 services, running IISRESET on all SharePoint servers in the farm, and even rebooting all the servers. There were no "other objects depend on it" as far as I can see. The issue remained.

The problem lies with a corrupted content database that needs to be cleaned up. As you can see below, when you run Get-SPContentDatabase, nothing is returned. However, when you run Get-SPDatabase, it reveals the database of type "Content Database" (you can ignore the SpFarmAdmin database, as that is for the content DB of Central Admin):

Another way to check the orphaned status is by running the Get-SPSite command. The output will show no value for the CompatibilityLevel column for the affected site (in this case, the top-level site collection):

The solution is to delete the orphaned database. You can do this by calling the Delete() method after obtaining the database by its ID (screenshot above). Once the orphaned databases are removed, the Remove-SPWebApplication command should run successfully: