I just went through the 10 usual forums I visit then Googled "CF card problems with HD DSLRs" and visited another 8 websites which discussed card use in HD DSLRs.
I did not find one report of a problem that related to card capacity. Plenty relating to cheap cards, too slow write speed cards and lazy use, (ie not reformatting the card in the camera before re-recording) but not one about this problem due to card capacity.
I use SanDisk Extreme UDMA 32Gb 60Mb/s cards, other guys I know and converse with a lot use 32Gb and 16Gb versions of the same card, none of us have had a single problem, yet. When I do hopefully it won't be a corrupted file on a 64Gb card with the last two days of shooting on it.
Cinematographer, Steadicam Operator, Final Cut Pro Post Production.
http://www.steadi-onfilms.com.au/