Hi,
If i am correct you want to do selective deletion in cube for some version which has been deleted in APO. For this do the following
1) There is a article in SCN to automate selective deletion (http://www.sdn.sap.com/irj/scn/go/portal/prtroot/docs/library/uuid/603a9558-0af1-2b10-86a3-c685c60071bc?overridelayout=true) using program. Create this program for all the infocube from which u want to do selective deletion
2) Create a Dynamic variant for all these program where version is read from TVARV table.
http://wiki.sdn.sap.com/wiki/display/ABAP/Creating+dynamic+variant+using+table+TVARV
3) Create a process chain in BW which is triggered by an event, with the above created program and the dynamic variant created for it
4) Create a FM in BW which inputs version, then changes the version value in TVARV to the input value of version and then triggers the event on which the process chain is scheduled to start using FM BP_EVENT_RAISE.
5) Now in APO side when you trigger your Tcode to delete a particular version make sure that you call the above created function module in BW thru remote RFC call by passing the version as input parameter.
6) Now once this FM is called in the pricess chain will start and then delete the values in infocube.
Regards,
Raghavendra.