Hi Sebastian,
your question doesn't make the problem very clear. You ask about WBS, but then describe the problem as being with the cost centre.
I'll try to point you towards some solutions anyway.
To begin with: all data in IT0027 is directly stored in PA0027 - I asume you know that, but just being safe.
The master cost centre is stored in IT0001. The field "master cost centre" above the lines to capture different cost assignments in the IT0027 screen is display only and shows data from IT0001. So, no matter, whether you create or copy a record in IT0027, the master cost centre is not stored there. If you think it is displaying the wrong value, double check how periods of 0027 and 0001 oberlap. To have a cleab display, one 0027 record should never cover more than one 0001 record. It may also be a refresh issue. Leave the transaction and go back in to be sure. however: no matter what's dilayed in that field, the master cost centre at any given point in time is always determinded from IT0001. So, this display field in 0027 doesn't matter anywhere.
This is completely different, if, for whatever reason, you capture the master cost centre in one of the lines in IT0027 and assign a percentage. Then it will never change automatically (assuming no BAdis or exits are used). One mistake made quite often is to capture a line with the residual percentage assigned to the master cost centre. This redundant information gets into your way, when the real master cost centre changes. It should not be done that way. The residual percentage of cost not assigned in any of the lines is automatically assigned to the master cost centre from IT0001.
Hope any of this helps to clarify how it works.
kind regards
Sven