I suspect your 5D is similar to my 450D in the respect...my 450D doesn't appear to have a separate internal clock battery.
edit actually found it has a CR2016 Lithium battery (but don't know where), which keeps clock time etc.
If I remove my battery it keeps time for a few days then looses it all. Installing the std battery and re-setting time..all good not problems many many days later.
I suspect the 5D is similar?
edit:
Annnndd I could be totally wrong..see
here. No memory battery under this panel for the 450D!