The upgrade of the Filenet Content Engine Server component for IBM Connections CR2 on Windows machines failed for two customers now. The command 'update-ce.bat -was.dm.path "D:\IBM\WebSphere\AppServer\profiles\Dmgr01" -was.admin.user wasadmin -was.admin.password password -ce.fp.installer.location "D:\INSTALL\CCMFIXCR2\5.2.1-P8CPE-WIN.EXE"' failed always with the message "Error: Please read the log for detail of the problem, it is D:\IBM\Connections\ccm\ccm\ccm\scripts\fn-ce-update.log".
If you look into the mentioned log you see that the deployment of the FileNetEngine application was successful. There is no hint why the procedure failed in the end.
I just ignored the error and went on with the next steps. I did not notice any problems and you will re-deploy a newer version manually as the last step anyway ... On Linux I never noticed that problem, so it seems to be something Windows specific.
By the way: A detailed instruction for upgrading COnnections 5.0 to CR2 can be found here. If you install on Windows make sure that you use a blank as separator instead of "=" (equal sign) for the Filenet upgrade procedures (e.g. use "-was.admin.user wasadmin" instead of "-was.admin.user=wasadmin")