BEX reporting incorrect figures after replicating objects

We have a process chain in BW that is run monthly and has been in production for a number of years with no issues.
After applying patches to our ERP6 system and upgrading to EHP4 - the process chain failed on a number of objects because the date & time stamp was different to the backend system.
I replicated the individual objects and the process chain ran successfully and the cube was available for reporting.
The business were not able to run their BEX queries as they were getting an error RFC_ERROR_SYSTEM_FAILURE TABLE_NOT_EXISTS
In BW, I ran program u201CSAP_DROP_TMPTABLESu201D. I Ticked every thing to make sure that all types of temp tables and temp reports were deleted.
The business were then able to run thier BEX queries but they said that their queries were not picking up all expected data.
The queries reported on employees with FTE headcount > 0 and Salary > 0.
I viewed the contents of the cube and I can see the employees with their FTE and Salary figures.
I ran the program u201CSAP_DROP_TMPTABLESu201D again and this time when the busines ran their BEX query it picked up the employees FTE figures but the salary is still not showing.
I have proved that the data is there by viewing the contents so what is the BEX query looking at and how can I get it to pick up the salary figures?
Edited by: Beverley Draper on Dec 29, 2011 2:43 PM
I forgot to mention that the employees who are not being picked up correctly by the BEX query have all had cost centre changes during last month. I don't see how this should affect it but it is something that they all have in common.
I have not been able to replicate the issue in our test or QA environment.
I need to assure the business that it will work when it is run again at month end on Sunday 31st December 2011. (Each time it is run it drops the cube and rebuilds it to contain 2 years worth of data).
Does any one have any ideas how I can get the BEX query to pick up the data that I can see when I view the contents of the cube?

thanks for the info.
There are no aggregates on the cube
I ran the users query in RSRT and I can see the data, however, the 17 employees that are being reported as missing by the business are showing their previous salary and the FTE for the current month is blank. (the business are only selecting people who have an FTE for the current month and a Salary)
If I run transaction RSA1 and then right click, manage then display the cube contents, it has got the correct salary and FTE for the 17 employees for the month of November.
FYI
These employees had a cost centre change on the last day of the month in November on R3 system but back dated to earlier in the month of November.
The monthly process chain ran late in the evening of 30th November which was after the changes to the employees cost centres had been made
I copied these employees to our QA system and ran the process chain and they all show the correct salary and FTE information.
I can only assume that by deleting the cube from RSA1 where it is available for reporting, and then re-running the job to create the cube again will correct it but the business do not want me to do this.
Is there any way I can refresh the data that the query is looking at because the cube has got the correct data?

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