I discovered the cause and solution for this.
The DeletePortalDesktopModules stored procedure is incorrect. It's missing conditions that cause this change.

You can run the following from the Host, SQL screen or from a SQL Management utility:

------
set QUOTED_IDENTIFIER ON
GO


ALTER PROCEDURE [dbo].[DeletePortalDesktopModules]
@PortalID int,
@DesktopModuleId int
AS
BEGIN
IF @PortalID is not null AND @DesktopModuleId is not null
DELETE FROM dbo.PortalDesktopModules WHERE PortalId = @PortalID AND DesktopModuleId = @DesktopModuleId
IF @PortalID is not null AND @DesktopModuleId is null
DELETE FROM dbo.PortalDesktopModules WHERE PortalId = @PortalID
IF @DesktopModuleId is not null AND @PortalID is null
DELETE FROM dbo.PortalDesktopModules WHERE DesktopModuleId = @DesktopModuleId
END
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The missing parts were the AND @xxx is null