Denish,
So any hint as why EE order are not deleted in ECC or How we can delete them in ECC?
This is a custom program; you are asking the wrong people. You should speak to the developer who created the program.
We can't know how this program was constructed. In general, if you delete something in APO and the deletion must be replicated in ECC, you must create your program such that this is done explicitly. If your developer had used, for instance, BAPI_MOSRVAPS_DELEMULTI to manage the deletion, there is a parameter in the BAPI that must be used. Your developer is responsible for knowing this and for making this happen within his code.
In most companies, such issues are handled as a standard change request or problem request.
Best Regards,
DB49