You don't mention which browser your using but most browsers I'm aware of not only keep the cookie file, but also an index file to the cookies. Have you tried recording teh timestamps on the file before you open it and doing a touch (or equivalent) to set it (them) back to their original values after you edited the file. Maybe the browser is checking dates.

Of course, it could also be doing a checksum of the contents, in which case your probably snookered.