Resolution:
If the schema of the IDoc is present in AESchema folder, R/3 adapter can publish the  IDoc even though the corresponding publisher service/endpoint is not configured in the Adapter instance.

Even when the adapter service is deleted the corresponding classes do not get deleted.  If the class references are there, it is able to publish the IDoc although it may not have the corresponding Idoc Publication endpoint. This behavior id due to the present default degin of the adapter. By default all the IDoc schemas for each of the Adapter instances in the project are created in the AESchema/ae/&ltkernel version of SAP App> folder.

In order to avoid this behavior of the adapter,

1) you can download the schema into a custom folder (AESchema/ae/&ltCustom Folder> for each of the adapter instances.

2) Use Unique programID for each of the adapter Publication instances.

Also, In order to remove the existing schema from the project, kindly follow the given below steps:-
1) Export the complete project into a dat file.
2) Open a new project.
3) Import the dat file (as in step 1) into this new project – Do not save this project.
4) Delete the classes that are not required.
5) Save the project.