When you replaced the CMOS battery you cleared the CMOS memory (where BIOS settings are stored) and so it's not at all surprising that the BIOS prompted you afterwards. The defaults used in most BIOSes are quite safe for the hardware, though possibly
less than ideal from a performance standpoint since they are generally very conservative. If you've never fiddled with the BIOS settings before then it's likely that the defaults are what you've always been using, so they just got re-loaded.
A dusty video card, especially if it's very dusty, can certainly cause the video card to fail to operate properly. Everything from heat to an obstructed fan, which are caused by dust buildup, can fry a video card or at least prevent it from running properly.
Edit to add:
If it ain't broke anymore, stop fixin' it!
Edited by Andrew, 10 November 2011 - 04:29 PM.