Assuming software version 3.87 was installed on the same PC as 3.59 was on, then the upgrade would have overwritten the 3.59 version, BUT not effected your configuration files which remain in the clients directory.
Recent versions of the B&O Configuration Tool have NOT conformed to the Microsoft standard of putting all installed programmes in the "Program Files" directory. I have a feeling that you may have previously installed a very old version which did go into the "Program Files" directory and it is that you have been changing without success.
Both version 3.59 and 3.87 are installed at:-
C:\Bang & Olufsen\Beo5 Configuration Tool
and you configuration file will be located at:-
C:\Bang & Olufsen\Beo5 Configuration Tool\Clients\2xxxxxxx
where xxxxxxxx is the serial number of your Beo5