Data Services 4.1 upgrade failed

Hi Everyone,
We came across a very really strange situation when we try to upgrade our DS from 4.0 SP3 to DS 4.1 SP2.
Before the upgrade, our DSConfig.txt file is in the bin folder where DS is installed (E:\SAP BusinessObject\Data Services\bin).  After the upgrade, we discovered a second DSConfig.txt file was created and saved to C:\Program Files\SAP BusinessObjects\Data Services\conf folder.  How is this possible when during the upgrade we specifically pointed to E:\SAP BusinessObject location?  More importantly which DSConfig.txt file should we use?  Right now we can't connect to our repositories through the CMC.
TIA

Also, do not worry about the change in the directory. In the release notes it  is mentioned that Linked path is changed to common directory path.
Configuration 
Old location:
<LINK_DIR>/bin/DSConfig.txt
New Location:
<DS_COMMON_DIR>/conf/DSCon
fig.txt
It is weird why SAP has to change the paths. I think your upgrade went well.
Please check the release notes documents for other changes.
http://help.sap.com/businessobject/product_guides/sboDS41/en/sbo411_ds_whats_new_en.pdf
Good Luck

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