This make sense.
In my case, The removal of application was getting failed because I was using one of send port in the Party which I was using to send files via AS2.
Correct me if I am wrong , I read somewhere over codeplex that we could actually automate the parties via deployment framework as well. but this might involved removal and creation of party every time we deploy...
Since the party is being used by many send ports of various applications , I decided not to include this in deployment and kept it as a manual task.
Now if a send port is associated to the party in biztalk, the famework cannot remove the application unless this association is removed and this is where I was getting the issue I mentioned above
Continue on Error on the task exe to True was a warning and the application deployment failed at a later stage trying to add the same application with existing name.
Here is the log you requested
Information: Removing application "APPL" from BizTalk configuration database (server="SERVER", database="BizTalkMgmtDb")... Error: Error while removing application "APPL". Error: Failed to delete resource(s).
Error: Change requests failed for some resources. Error: Unable to process delete change request for BizTalk binding "". Import bindings (unbind) failed. Error: Failed to update binding information. Error: Column 'nvcName' does
not belong to table bts_party_sendport. Command failed with 1 errors, 0 warnings. MSBUILD : warning MSB3073: The command "BTSTask.exe RemoveApp -ApplicationName:"APPL"" exited with code 1. [D:\APPL\Deployment\Deployment.btdfproj]
The previous error was converted to a warning because the task was called with ContinueOnError=true. Build continuing because "ContinueOnError" on the task "Exec" is set to "true".