Thanks for the Input Alex.... It is True that there has been given some thought of making it a module integration... but the sub DotNet application is has to be stand-a-lone sub application at this time and the module approach is just not an option due to complications of the child application.

The application has to run separate as a child app software just as it has been doing prior to our 4.7 upgrade. That is a expicit requirement and Integration is Not and Option.
We would just like to know what changed between 4.7 and 4.9 that makes runing a child application cause the script manager in 4.9+ to Fail horribly.
Something about DNN core changed in 4.9

At this time we have a critical system down because of the change and although in the future we can whip out the white marker board and re-write our secondary application as a module, at this time and because of the complexity of the dotnet software we are trying to run as a child application its just not an option.

We are still trying to find a fix to this solution to restore our complex dotnet software we had running before the upgrade. The Module or IFRAME approach is just not an option at this time. We are still trying to get this working again.